Starting phenix.real_space_refine on Sat Aug 23 15:34:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqb_40701/08_2025/8sqb_40701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqb_40701/08_2025/8sqb_40701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sqb_40701/08_2025/8sqb_40701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqb_40701/08_2025/8sqb_40701.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqb_40701/08_2025/8sqb_40701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqb_40701/08_2025/8sqb_40701.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.049 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 36 5.16 5 C 8168 2.51 5 N 2230 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12991 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6045 Classifications: {'peptide': 765} Link IDs: {'CIS': 2, 'PTRANS': 28, 'TRANS': 734} Chain breaks: 5 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2776 Classifications: {'peptide': 369} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 1318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1309 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 171, 1309 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 3 bond proxies already assigned to first conformer: 1319 Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1740 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "F" Number of atoms: 418 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 67, 410 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 67, 410 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 401 Time building chain proxies: 2.94, per 1000 atoms: 0.23 Number of scatterers: 12991 At special positions: 0 Unit cell: (114.48, 132.84, 130.68, 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 36 16.00 O 2557 8.00 N 2230 7.00 C 8168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS F1172 " 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: 0.72 Conformation dependent library (CDL) restraints added in 427.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 22.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.670A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.775A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.797A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.785A pdb=" N SER C 122 " --> pdb=" O PRO C 118 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 207 removed outlier: 3.731A pdb=" N SER C 198 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 4.163A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 removed outlier: 4.230A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.818A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.500A pdb=" N ALA D 163 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.796A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.784A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 3.935A pdb=" N ARG A 76 " --> pdb=" O GLN A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 182 removed outlier: 3.654A pdb=" N ILE A 254 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 267 through 271 current: chain 'A' and resid 334 through 341 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.822A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.936A pdb=" N GLN A 445 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 459 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 470 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY A 510 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 509 " --> pdb=" O HIS A 533 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 528 " --> pdb=" O ASN A 573 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 564 through 574 current: chain 'A' and resid 592 through 600 removed outlier: 3.738A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 596 " --> pdb=" O THR A 612 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 609 through 615 current: chain 'A' and resid 628 through 635 removed outlier: 3.572A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 630 " --> pdb=" O GLU A 717 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 632 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 784 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA8, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.796A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 162 removed outlier: 4.136A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.875A pdb=" N VAL B 209 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.787A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.621A pdb=" N ASP B 292 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.631A pdb=" N HIS B 347 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 142 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 142 current: chain 'C' and resid 158 through 164 removed outlier: 5.028A pdb=" N ARG C 158 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 182 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 32 through 34 current: chain 'E' and resid 73 through 80 Processing sheet with id=AB9, first strand: chain 'F' and resid 1265 through 1267 386 hydrogen bonds defined for protein. 1029 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: 1.94 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4365 1.34 - 1.46: 2851 1.46 - 1.57: 5970 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13255 Sorted by residual: bond pdb=" C ASP D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 1.332 1.310 0.023 8.20e-03 1.49e+04 7.56e+00 bond pdb=" CB TRP D 191 " pdb=" CG TRP D 191 " ideal model delta sigma weight residual 1.498 1.426 0.072 3.10e-02 1.04e+03 5.41e+00 bond pdb=" C THR B 386 " pdb=" N VAL B 387 " ideal model delta sigma weight residual 1.329 1.286 0.043 2.19e-02 2.09e+03 3.86e+00 bond pdb=" CB TRP A 449 " pdb=" CG TRP A 449 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.46e+00 ... (remaining 13250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 17691 2.53 - 5.06: 285 5.06 - 7.59: 24 7.59 - 10.12: 2 10.12 - 12.65: 4 Bond angle restraints: 18006 Sorted by residual: angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.21 107.00 6.21 1.15e+00 7.56e-01 2.91e+01 angle pdb=" C GLY C 169 " pdb=" N TYR C 170 " pdb=" CA TYR C 170 " ideal model delta sigma weight residual 121.70 130.09 -8.39 1.80e+00 3.09e-01 2.17e+01 angle pdb=" N ILE C 82 " pdb=" CA ILE C 82 " pdb=" C ILE C 82 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N GLY B 354 " pdb=" CA GLY B 354 " pdb=" C GLY B 354 " ideal model delta sigma weight residual 113.30 102.53 10.77 2.90e+00 1.19e-01 1.38e+01 angle pdb=" CA TRP B 228 " pdb=" CB TRP B 228 " pdb=" CG TRP B 228 " ideal model delta sigma weight residual 113.60 120.62 -7.02 1.90e+00 2.77e-01 1.36e+01 ... (remaining 18001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7007 17.96 - 35.92: 687 35.92 - 53.88: 110 53.88 - 71.83: 19 71.83 - 89.79: 16 Dihedral angle restraints: 7839 sinusoidal: 3026 harmonic: 4813 Sorted by residual: dihedral pdb=" CA ILE B 227 " pdb=" C ILE B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta harmonic sigma weight residual 180.00 129.11 50.89 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA ASP B 300 " pdb=" C ASP B 300 " pdb=" N GLN B 301 " pdb=" CA GLN B 301 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ARG A 346 " pdb=" C ARG A 346 " pdb=" N PHE A 347 " pdb=" CA PHE A 347 " ideal model delta harmonic sigma weight residual 180.00 -152.91 -27.09 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 7836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1266 0.038 - 0.077: 508 0.077 - 0.115: 169 0.115 - 0.153: 29 0.153 - 0.192: 6 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CB ILE D 35 " pdb=" CA ILE D 35 " pdb=" CG1 ILE D 35 " pdb=" CG2 ILE D 35 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA THR B 37 " pdb=" N THR B 37 " pdb=" C THR B 37 " pdb=" CB THR B 37 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA TYR C 170 " pdb=" N TYR C 170 " pdb=" C TYR C 170 " pdb=" CB TYR C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1975 not shown) Planarity restraints: 2374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 60 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C VAL C 60 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL C 60 " -0.012 2.00e-02 2.50e+03 pdb=" N THR C 61 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 437 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLY A 437 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 437 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 438 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 104 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE B 104 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 104 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 104 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 104 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 104 " 0.004 2.00e-02 2.50e+03 ... (remaining 2371 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 325 2.53 - 3.12: 12262 3.12 - 3.71: 21776 3.71 - 4.31: 28364 4.31 - 4.90: 44270 Nonbonded interactions: 106997 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" O VAL B 286 " model vdw 1.936 3.040 nonbonded pdb=" OG1 THR A 505 " pdb=" O SER A 537 " model vdw 1.990 3.040 nonbonded pdb=" O ASN E 41 " pdb=" OG SER E 44 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR B 309 " pdb=" OD1 ASP B 311 " model vdw 2.082 3.040 nonbonded pdb=" OG1 THR E 92 " pdb=" OD2 ASP E 105 " model vdw 2.088 3.040 ... (remaining 106992 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 0.072 13256 Z= 0.387 Angle : 0.840 12.652 18008 Z= 0.464 Chirality : 0.046 0.192 1978 Planarity : 0.004 0.040 2374 Dihedral : 14.861 89.793 4768 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 33.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.27 % Favored : 80.61 % Rotamer: Outliers : 1.02 % Allowed : 12.37 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.64 (0.16), residues: 1643 helix: -2.42 (0.22), residues: 334 sheet: -4.20 (0.20), residues: 410 loop : -4.17 (0.16), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 321 TYR 0.018 0.002 TYR A 757 PHE 0.029 0.002 PHE B 104 TRP 0.028 0.002 TRP B 228 HIS 0.007 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00793 (13255) covalent geometry : angle 0.83985 (18006) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.38200 ( 2) hydrogen bonds : bond 0.22303 ( 386) hydrogen bonds : angle 9.06043 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8677 (m-10) cc_final: 0.8270 (m-80) REVERT: A 147 TYR cc_start: 0.8563 (m-80) cc_final: 0.8354 (m-80) REVERT: A 325 MET cc_start: 0.7521 (ptp) cc_final: 0.6478 (ppp) REVERT: A 396 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8233 (mm-30) REVERT: A 801 GLN cc_start: 0.7478 (mt0) cc_final: 0.6817 (mt0) REVERT: B 42 PHE cc_start: 0.3713 (OUTLIER) cc_final: 0.3171 (m-10) REVERT: B 127 GLU cc_start: 0.8053 (tp30) cc_final: 0.7804 (tp30) REVERT: B 221 MET cc_start: 0.8661 (mtp) cc_final: 0.8454 (mtt) REVERT: B 278 MET cc_start: 0.5808 (mmt) cc_final: 0.5419 (tpp) REVERT: B 289 PHE cc_start: 0.7745 (p90) cc_final: 0.7444 (p90) REVERT: C 127 LYS cc_start: 0.6591 (mmtt) cc_final: 0.6293 (mppt) REVERT: C 202 MET cc_start: 0.6865 (mmt) cc_final: 0.6557 (mmt) REVERT: D 176 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7364 (ttmm) REVERT: D 191 TRP cc_start: 0.8730 (m-10) cc_final: 0.8238 (m-10) REVERT: D 199 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6943 (tm-30) REVERT: E 87 THR cc_start: 0.8200 (t) cc_final: 0.7918 (p) REVERT: E 104 ILE cc_start: 0.7731 (pt) cc_final: 0.7502 (mp) outliers start: 10 outliers final: 7 residues processed: 211 average time/residue: 0.0982 time to fit residues: 30.1347 Evaluate side-chains 144 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN A 678 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091425 restraints weight = 78228.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.091930 restraints weight = 44490.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093692 restraints weight = 28781.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094898 restraints weight = 18522.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095086 restraints weight = 16202.879| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13256 Z= 0.179 Angle : 0.719 8.202 18008 Z= 0.376 Chirality : 0.046 0.230 1978 Planarity : 0.004 0.045 2374 Dihedral : 6.457 53.773 1839 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 3.78 % Allowed : 14.70 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.39 (0.18), residues: 1643 helix: -0.76 (0.25), residues: 351 sheet: -3.61 (0.22), residues: 372 loop : -3.62 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 120 TYR 0.022 0.002 TYR A 454 PHE 0.024 0.002 PHE B 104 TRP 0.034 0.002 TRP B 228 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00391 (13255) covalent geometry : angle 0.71944 (18006) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.77594 ( 2) hydrogen bonds : bond 0.04878 ( 386) hydrogen bonds : angle 6.06423 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.8349 (m-80) cc_final: 0.8131 (m-80) REVERT: A 663 PHE cc_start: 0.8259 (m-80) cc_final: 0.7998 (m-80) REVERT: B 32 MET cc_start: 0.7163 (pmm) cc_final: 0.6563 (pmm) REVERT: B 76 ASP cc_start: 0.8487 (p0) cc_final: 0.8057 (p0) REVERT: B 296 ILE cc_start: 0.8188 (mp) cc_final: 0.7978 (tt) REVERT: C 202 MET cc_start: 0.6510 (mmt) cc_final: 0.5817 (mmt) REVERT: E 33 ASN cc_start: 0.8039 (p0) cc_final: 0.7640 (p0) outliers start: 48 outliers final: 27 residues processed: 213 average time/residue: 0.0865 time to fit residues: 27.8111 Evaluate side-chains 169 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 301 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 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 = 0.3716 r_free = 0.3716 target = 0.115683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092955 restraints weight = 70640.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093943 restraints weight = 59105.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095955 restraints weight = 32476.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096836 restraints weight = 20784.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097396 restraints weight = 17535.302| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13256 Z= 0.156 Angle : 0.676 7.693 18008 Z= 0.351 Chirality : 0.045 0.177 1978 Planarity : 0.004 0.039 2374 Dihedral : 6.125 57.531 1835 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 4.00 % Allowed : 17.98 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.19), residues: 1643 helix: 0.11 (0.27), residues: 354 sheet: -3.48 (0.21), residues: 397 loop : -3.27 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.018 0.002 TYR A 504 PHE 0.021 0.001 PHE A 478 TRP 0.028 0.002 TRP B 228 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00346 (13255) covalent geometry : angle 0.67599 (18006) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.45105 ( 2) hydrogen bonds : bond 0.04321 ( 386) hydrogen bonds : angle 5.40202 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.7947 (m-80) cc_final: 0.7364 (m-80) REVERT: A 663 PHE cc_start: 0.8321 (m-80) cc_final: 0.8102 (m-80) REVERT: B 32 MET cc_start: 0.7074 (pmm) cc_final: 0.6622 (pmm) REVERT: B 76 ASP cc_start: 0.8341 (p0) cc_final: 0.7969 (p0) REVERT: C 78 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8409 (mmtt) REVERT: C 202 MET cc_start: 0.6775 (mmt) cc_final: 0.6150 (mmt) REVERT: D 34 GLU cc_start: 0.7634 (pm20) cc_final: 0.7245 (mp0) REVERT: E 33 ASN cc_start: 0.8241 (p0) cc_final: 0.7800 (p0) outliers start: 51 outliers final: 37 residues processed: 213 average time/residue: 0.0837 time to fit residues: 27.7570 Evaluate side-chains 182 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 68 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 45 optimal weight: 0.0370 chunk 153 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 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 = 0.3862 r_free = 0.3862 target = 0.121191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095178 restraints weight = 100591.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097964 restraints weight = 43163.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099204 restraints weight = 23612.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100007 restraints weight = 16100.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102536 restraints weight = 13501.303| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13256 Z= 0.131 Angle : 0.645 8.323 18008 Z= 0.333 Chirality : 0.044 0.155 1978 Planarity : 0.004 0.037 2374 Dihedral : 5.886 59.788 1835 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 4.15 % Allowed : 20.01 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.19), residues: 1643 helix: 0.29 (0.27), residues: 360 sheet: -3.13 (0.22), residues: 398 loop : -3.11 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.026 0.001 TYR C 197 PHE 0.021 0.001 PHE A 478 TRP 0.038 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00289 (13255) covalent geometry : angle 0.64500 (18006) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.34897 ( 2) hydrogen bonds : bond 0.03956 ( 386) hydrogen bonds : angle 5.01802 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8223 (m-10) cc_final: 0.7708 (m-80) REVERT: A 488 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7195 (ttt-90) REVERT: A 545 MET cc_start: 0.8244 (tpp) cc_final: 0.7981 (tpp) REVERT: A 546 TRP cc_start: 0.7361 (m100) cc_final: 0.6759 (m-10) REVERT: A 552 MET cc_start: 0.8758 (mtp) cc_final: 0.8377 (mtp) REVERT: B 32 MET cc_start: 0.7140 (pmm) cc_final: 0.6748 (pmm) REVERT: B 76 ASP cc_start: 0.8275 (p0) cc_final: 0.7937 (p0) REVERT: C 202 MET cc_start: 0.6859 (mmt) cc_final: 0.6365 (mmt) outliers start: 53 outliers final: 40 residues processed: 206 average time/residue: 0.0832 time to fit residues: 26.5560 Evaluate side-chains 189 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 159 optimal weight: 50.0000 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.118209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091897 restraints weight = 74207.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093537 restraints weight = 32292.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094827 restraints weight = 21121.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095363 restraints weight = 15920.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095929 restraints weight = 13898.974| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13256 Z= 0.197 Angle : 0.682 7.489 18008 Z= 0.355 Chirality : 0.045 0.168 1978 Planarity : 0.004 0.038 2374 Dihedral : 6.029 57.463 1834 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 5.68 % Allowed : 20.82 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.19), residues: 1643 helix: 0.25 (0.27), residues: 360 sheet: -3.14 (0.22), residues: 420 loop : -3.08 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.024 0.002 TYR C 41 PHE 0.025 0.002 PHE A 478 TRP 0.049 0.002 TRP D 191 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00435 (13255) covalent geometry : angle 0.68238 (18006) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.57298 ( 2) hydrogen bonds : bond 0.04326 ( 386) hydrogen bonds : angle 5.07063 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8529 (mm-30) REVERT: A 142 TYR cc_start: 0.8237 (m-10) cc_final: 0.7729 (m-80) REVERT: A 304 MET cc_start: 0.8739 (ttm) cc_final: 0.8443 (ttm) REVERT: A 552 MET cc_start: 0.8891 (mtp) cc_final: 0.8628 (mtp) REVERT: B 32 MET cc_start: 0.7299 (pmm) cc_final: 0.6804 (pmm) REVERT: B 76 ASP cc_start: 0.8463 (p0) cc_final: 0.8072 (p0) REVERT: B 171 LEU cc_start: 0.8376 (mp) cc_final: 0.7995 (mt) REVERT: C 57 ILE cc_start: 0.8946 (mm) cc_final: 0.8635 (mt) REVERT: C 202 MET cc_start: 0.6687 (mmt) cc_final: 0.6230 (mmt) REVERT: C 205 ILE cc_start: 0.8882 (mm) cc_final: 0.8588 (mt) REVERT: D 34 GLU cc_start: 0.7810 (pm20) cc_final: 0.7383 (mp0) REVERT: D 80 TYR cc_start: 0.9226 (t80) cc_final: 0.8948 (t80) outliers start: 74 outliers final: 56 residues processed: 209 average time/residue: 0.0751 time to fit residues: 24.9271 Evaluate side-chains 201 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 0.0970 chunk 84 optimal weight: 0.0670 chunk 109 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** B 287 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.119648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091845 restraints weight = 81378.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094794 restraints weight = 29889.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095912 restraints weight = 17628.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096517 restraints weight = 14019.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097067 restraints weight = 12167.903| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13256 Z= 0.116 Angle : 0.638 9.649 18008 Z= 0.326 Chirality : 0.044 0.163 1978 Planarity : 0.004 0.034 2374 Dihedral : 5.679 55.899 1834 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.22 % Allowed : 21.91 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.20), residues: 1643 helix: 0.64 (0.28), residues: 353 sheet: -2.94 (0.22), residues: 431 loop : -2.86 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 83 TYR 0.021 0.001 TYR A 504 PHE 0.023 0.001 PHE A 478 TRP 0.028 0.001 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00254 (13255) covalent geometry : angle 0.63782 (18006) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.25573 ( 2) hydrogen bonds : bond 0.03681 ( 386) hydrogen bonds : angle 4.72973 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8274 (m-10) cc_final: 0.7702 (m-80) REVERT: A 191 ASP cc_start: 0.8758 (p0) cc_final: 0.7719 (t0) REVERT: A 192 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: A 546 TRP cc_start: 0.7313 (m100) cc_final: 0.6664 (m-10) REVERT: B 32 MET cc_start: 0.7342 (pmm) cc_final: 0.6872 (pmm) REVERT: B 76 ASP cc_start: 0.8162 (p0) cc_final: 0.7859 (p0) REVERT: B 171 LEU cc_start: 0.8540 (mp) cc_final: 0.8143 (mt) REVERT: B 248 ASP cc_start: 0.6423 (m-30) cc_final: 0.5774 (p0) REVERT: B 249 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7084 (p) REVERT: B 261 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8249 (tp) REVERT: C 57 ILE cc_start: 0.8911 (mm) cc_final: 0.8597 (mt) REVERT: C 202 MET cc_start: 0.6564 (mmt) cc_final: 0.6273 (mmt) REVERT: C 205 ILE cc_start: 0.8795 (mm) cc_final: 0.8548 (mt) REVERT: E 33 ASN cc_start: 0.8324 (p0) cc_final: 0.7898 (p0) REVERT: E 67 PRO cc_start: 0.8925 (Cg_endo) cc_final: 0.8693 (Cg_exo) outliers start: 54 outliers final: 42 residues processed: 217 average time/residue: 0.0757 time to fit residues: 26.1227 Evaluate side-chains 193 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 71 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 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 = 0.3793 r_free = 0.3793 target = 0.117519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089778 restraints weight = 85254.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092532 restraints weight = 30721.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093972 restraints weight = 18000.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094418 restraints weight = 14117.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095086 restraints weight = 12174.621| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13256 Z= 0.160 Angle : 0.667 9.355 18008 Z= 0.346 Chirality : 0.044 0.170 1978 Planarity : 0.004 0.036 2374 Dihedral : 5.743 55.144 1834 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 4.88 % Allowed : 23.00 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.20), residues: 1643 helix: 0.51 (0.28), residues: 355 sheet: -2.88 (0.22), residues: 430 loop : -2.83 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.036 0.002 TYR C 157 PHE 0.025 0.002 PHE A 478 TRP 0.052 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00356 (13255) covalent geometry : angle 0.66653 (18006) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.31397 ( 2) hydrogen bonds : bond 0.03940 ( 386) hydrogen bonds : angle 4.78799 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8617 (mm-30) REVERT: A 142 TYR cc_start: 0.8292 (m-10) cc_final: 0.7798 (m-80) REVERT: A 192 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.7556 (pp20) REVERT: B 32 MET cc_start: 0.7465 (pmm) cc_final: 0.6975 (pmm) REVERT: B 76 ASP cc_start: 0.8357 (p0) cc_final: 0.8053 (p0) REVERT: B 171 LEU cc_start: 0.8471 (mp) cc_final: 0.8105 (mt) REVERT: B 249 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7240 (p) REVERT: B 261 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8295 (tp) REVERT: C 57 ILE cc_start: 0.8928 (mm) cc_final: 0.8620 (mt) REVERT: C 129 TYR cc_start: 0.6320 (m-10) cc_final: 0.5930 (m-80) REVERT: C 205 ILE cc_start: 0.8697 (mm) cc_final: 0.8428 (mt) REVERT: E 67 PRO cc_start: 0.8939 (Cg_endo) cc_final: 0.8646 (Cg_exo) outliers start: 63 outliers final: 50 residues processed: 201 average time/residue: 0.0851 time to fit residues: 27.0765 Evaluate side-chains 196 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 63 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 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 = 0.3828 r_free = 0.3828 target = 0.119984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092353 restraints weight = 90789.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095329 restraints weight = 33384.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096530 restraints weight = 18915.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.097353 restraints weight = 14570.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097875 restraints weight = 12348.753| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13256 Z= 0.125 Angle : 0.643 8.489 18008 Z= 0.333 Chirality : 0.044 0.184 1978 Planarity : 0.004 0.037 2374 Dihedral : 5.561 54.216 1834 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 4.66 % Allowed : 23.07 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.20), residues: 1643 helix: 0.70 (0.28), residues: 356 sheet: -2.70 (0.23), residues: 420 loop : -2.81 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 203 TYR 0.031 0.001 TYR C 157 PHE 0.022 0.001 PHE A 478 TRP 0.038 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00278 (13255) covalent geometry : angle 0.64269 (18006) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.26048 ( 2) hydrogen bonds : bond 0.03603 ( 386) hydrogen bonds : angle 4.59752 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8220 (m-10) cc_final: 0.7686 (m-80) REVERT: A 191 ASP cc_start: 0.8726 (p0) cc_final: 0.7686 (t0) REVERT: A 192 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: A 754 TYR cc_start: 0.5015 (m-10) cc_final: 0.4756 (m-10) REVERT: B 32 MET cc_start: 0.7420 (pmm) cc_final: 0.6912 (pmm) REVERT: B 76 ASP cc_start: 0.8198 (p0) cc_final: 0.7917 (p0) REVERT: B 261 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8269 (tp) REVERT: C 57 ILE cc_start: 0.8894 (mm) cc_final: 0.8583 (mt) REVERT: D 34 GLU cc_start: 0.8150 (pm20) cc_final: 0.7944 (mp0) REVERT: D 109 MET cc_start: 0.7915 (mtt) cc_final: 0.7468 (mtt) REVERT: E 67 PRO cc_start: 0.8874 (Cg_endo) cc_final: 0.8630 (Cg_exo) outliers start: 60 outliers final: 54 residues processed: 204 average time/residue: 0.0822 time to fit residues: 26.9295 Evaluate side-chains 196 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 26 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.121719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094452 restraints weight = 82803.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096715 restraints weight = 30161.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097866 restraints weight = 18538.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098197 restraints weight = 14028.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098559 restraints weight = 12436.408| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13256 Z= 0.116 Angle : 0.639 8.856 18008 Z= 0.329 Chirality : 0.043 0.174 1978 Planarity : 0.004 0.034 2374 Dihedral : 5.340 53.598 1832 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 4.29 % Allowed : 24.02 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.20), residues: 1643 helix: 0.79 (0.28), residues: 356 sheet: -2.63 (0.23), residues: 415 loop : -2.72 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 203 TYR 0.024 0.001 TYR C 157 PHE 0.024 0.001 PHE A 478 TRP 0.031 0.001 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00258 (13255) covalent geometry : angle 0.63855 (18006) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.15579 ( 2) hydrogen bonds : bond 0.03464 ( 386) hydrogen bonds : angle 4.50308 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8844 (ttp) cc_final: 0.8589 (tpt) REVERT: A 115 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8609 (mm-30) REVERT: A 142 TYR cc_start: 0.8256 (m-10) cc_final: 0.7638 (m-80) REVERT: A 191 ASP cc_start: 0.8726 (p0) cc_final: 0.7688 (t0) REVERT: A 192 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: B 76 ASP cc_start: 0.8172 (p0) cc_final: 0.7929 (p0) REVERT: B 249 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.6989 (p) REVERT: B 261 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8255 (tp) REVERT: C 57 ILE cc_start: 0.8904 (mm) cc_final: 0.8571 (mt) REVERT: C 194 MET cc_start: 0.6196 (tmm) cc_final: 0.5781 (tmm) REVERT: C 205 ILE cc_start: 0.8663 (mm) cc_final: 0.8361 (mt) REVERT: D 109 MET cc_start: 0.7927 (mtt) cc_final: 0.7474 (mtt) REVERT: D 111 MET cc_start: 0.8526 (mpp) cc_final: 0.8255 (mpp) outliers start: 55 outliers final: 48 residues processed: 203 average time/residue: 0.0773 time to fit residues: 25.4925 Evaluate side-chains 197 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 0.5980 chunk 153 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 25 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095835 restraints weight = 76238.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098501 restraints weight = 27123.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099972 restraints weight = 16021.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100140 restraints weight = 12136.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100668 restraints weight = 10803.555| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13256 Z= 0.114 Angle : 0.637 9.058 18008 Z= 0.329 Chirality : 0.043 0.178 1978 Planarity : 0.004 0.034 2374 Dihedral : 5.230 52.877 1832 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.49 % Allowed : 25.40 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.20), residues: 1643 helix: 0.91 (0.29), residues: 351 sheet: -2.58 (0.23), residues: 418 loop : -2.58 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 203 TYR 0.024 0.001 TYR C 157 PHE 0.024 0.001 PHE A 478 TRP 0.030 0.001 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00256 (13255) covalent geometry : angle 0.63708 (18006) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.15951 ( 2) hydrogen bonds : bond 0.03394 ( 386) hydrogen bonds : angle 4.50120 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8800 (ttp) cc_final: 0.8185 (tmm) REVERT: A 114 LEU cc_start: 0.9562 (mt) cc_final: 0.9305 (pp) REVERT: A 115 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 191 ASP cc_start: 0.8687 (p0) cc_final: 0.7730 (t0) REVERT: A 192 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: A 552 MET cc_start: 0.8505 (mtp) cc_final: 0.8177 (mtp) REVERT: A 554 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6428 (mp0) REVERT: B 261 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (tp) REVERT: C 57 ILE cc_start: 0.8891 (mm) cc_final: 0.8566 (mt) REVERT: C 205 ILE cc_start: 0.8684 (mm) cc_final: 0.8479 (mt) REVERT: D 80 TYR cc_start: 0.9061 (t80) cc_final: 0.8809 (t80) REVERT: D 109 MET cc_start: 0.7911 (mtt) cc_final: 0.7505 (mtt) REVERT: D 111 MET cc_start: 0.8500 (mpp) cc_final: 0.8228 (mpp) REVERT: D 176 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8276 (ttmm) REVERT: D 232 GLU cc_start: 0.8280 (tp30) cc_final: 0.7878 (tm-30) outliers start: 44 outliers final: 40 residues processed: 202 average time/residue: 0.0956 time to fit residues: 30.5825 Evaluate side-chains 194 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 110 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 113 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.122752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095446 restraints weight = 86360.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099592 restraints weight = 33032.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100323 restraints weight = 16859.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.101123 restraints weight = 13048.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101812 restraints weight = 10998.529| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13256 Z= 0.123 Angle : 0.646 8.694 18008 Z= 0.336 Chirality : 0.044 0.238 1978 Planarity : 0.004 0.036 2374 Dihedral : 5.227 52.636 1832 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.00 % Allowed : 25.55 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.20), residues: 1643 helix: 0.91 (0.28), residues: 351 sheet: -2.49 (0.23), residues: 415 loop : -2.56 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 203 TYR 0.022 0.001 TYR A 504 PHE 0.025 0.001 PHE A 478 TRP 0.052 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00278 (13255) covalent geometry : angle 0.64601 (18006) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.10648 ( 2) hydrogen bonds : bond 0.03460 ( 386) hydrogen bonds : angle 4.50563 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.85 seconds wall clock time: 35 minutes 1.55 seconds (2101.55 seconds total)