Starting phenix.real_space_refine on Thu May 15 10:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqb_40701/05_2025/8sqb_40701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqb_40701/05_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_40701/05_2025/8sqb_40701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqb_40701/05_2025/8sqb_40701.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqb_40701/05_2025/8sqb_40701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqb_40701/05_2025/8sqb_40701.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 401 Time building chain proxies: 7.76, per 1000 atoms: 0.60 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: 3.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.35 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: 4.47 Time building geometry restraints manager: 3.74 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.860 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- 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 : 33.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.002 TRP B 228 HIS 0.007 0.001 HIS A 677 PHE 0.029 0.002 PHE B 104 TYR 0.018 0.002 TYR A 757 ARG 0.010 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.22303 ( 386) hydrogen bonds : angle 9.06043 ( 1029) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.38200 ( 2) covalent geometry : bond 0.00793 (13255) covalent geometry : angle 0.83985 (18006) *********************** 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 : 1.513 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: 0.2641 time to fit residues: 79.2097 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 : 1.562 ------------------------------------------------------------------------------- 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 138 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.114671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089676 restraints weight = 93393.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091048 restraints weight = 50843.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092845 restraints weight = 30349.721| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1982 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= 0.178 Angle : 0.716 8.349 18008 Z= 0.374 Chirality : 0.046 0.226 1978 Planarity : 0.004 0.044 2374 Dihedral : 6.469 53.184 1839 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 3.71 % Allowed : 14.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.18), residues: 1643 helix: -0.78 (0.25), residues: 351 sheet: -3.62 (0.22), residues: 372 loop : -3.64 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 228 HIS 0.005 0.001 HIS A 533 PHE 0.024 0.002 PHE B 104 TYR 0.021 0.002 TYR A 454 ARG 0.006 0.001 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 386) hydrogen bonds : angle 6.12769 ( 1029) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.69337 ( 2) covalent geometry : bond 0.00387 (13255) covalent geometry : angle 0.71625 (18006) *********************** 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: 47 poor density : 179 time to evaluate : 1.352 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: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.8388 (m-80) cc_final: 0.8142 (m-80) REVERT: A 663 PHE cc_start: 0.8299 (m-80) cc_final: 0.7990 (m-80) REVERT: A 801 GLN cc_start: 0.8056 (mt0) cc_final: 0.7839 (mp10) REVERT: B 32 MET cc_start: 0.7175 (pmm) cc_final: 0.6565 (pmm) REVERT: B 76 ASP cc_start: 0.8572 (p0) cc_final: 0.8131 (p0) REVERT: B 296 ILE cc_start: 0.8073 (mp) cc_final: 0.7842 (tt) REVERT: C 202 MET cc_start: 0.6631 (mmt) cc_final: 0.5910 (mmt) REVERT: D 52 ILE cc_start: 0.8327 (mt) cc_final: 0.7910 (mt) REVERT: D 53 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8842 (t) REVERT: E 33 ASN cc_start: 0.8084 (p0) cc_final: 0.7693 (p0) outliers start: 47 outliers final: 25 residues processed: 213 average time/residue: 0.2196 time to fit residues: 69.5579 Evaluate side-chains 173 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 759 ASP 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 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 D residue 53 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 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 100 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 9.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.117457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091921 restraints weight = 79027.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093601 restraints weight = 39747.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.094893 restraints weight = 26385.127| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 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 = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13256 Z= 0.133 Angle : 0.658 7.704 18008 Z= 0.341 Chirality : 0.045 0.174 1978 Planarity : 0.004 0.039 2374 Dihedral : 5.963 56.500 1835 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 3.28 % Allowed : 18.27 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.19), residues: 1643 helix: 0.17 (0.27), residues: 354 sheet: -3.34 (0.22), residues: 389 loop : -3.26 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.020 0.001 PHE A 478 TYR 0.019 0.001 TYR A 504 ARG 0.006 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 386) hydrogen bonds : angle 5.29556 ( 1029) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.36175 ( 2) covalent geometry : bond 0.00294 (13255) covalent geometry : angle 0.65840 (18006) *********************** 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 222 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8040 (m-80) cc_final: 0.7421 (m-80) REVERT: A 546 TRP cc_start: 0.7315 (m100) cc_final: 0.6742 (m-10) REVERT: A 663 PHE cc_start: 0.8326 (m-80) cc_final: 0.8103 (m-80) REVERT: B 76 ASP cc_start: 0.8231 (p0) cc_final: 0.7947 (p0) REVERT: C 78 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8342 (mmtt) REVERT: C 202 MET cc_start: 0.6754 (mmt) cc_final: 0.6194 (mmt) REVERT: D 34 GLU cc_start: 0.7648 (pm20) cc_final: 0.7230 (mp0) REVERT: E 33 ASN cc_start: 0.8133 (p0) cc_final: 0.7766 (p0) REVERT: E 103 ASN cc_start: 0.7468 (m110) cc_final: 0.7209 (m-40) outliers start: 41 outliers final: 27 residues processed: 215 average time/residue: 0.2016 time to fit residues: 65.9343 Evaluate side-chains 180 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 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 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 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain D residue 27 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 92 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 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 = 0.3794 r_free = 0.3794 target = 0.116723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090598 restraints weight = 81621.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092024 restraints weight = 36951.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093369 restraints weight = 23815.497| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13256 Z= 0.239 Angle : 0.725 8.892 18008 Z= 0.379 Chirality : 0.046 0.168 1978 Planarity : 0.004 0.040 2374 Dihedral : 6.312 58.935 1834 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.82 % Favored : 85.18 % Rotamer: Outliers : 5.31 % Allowed : 19.07 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.19), residues: 1643 helix: 0.20 (0.27), residues: 351 sheet: -3.30 (0.21), residues: 425 loop : -3.22 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 191 HIS 0.005 0.001 HIS A 677 PHE 0.021 0.002 PHE B 104 TYR 0.029 0.002 TYR C 157 ARG 0.005 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 386) hydrogen bonds : angle 5.38466 ( 1029) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.73050 ( 2) covalent geometry : bond 0.00530 (13255) covalent geometry : angle 0.72489 (18006) *********************** 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 226 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7303 (ptp90) cc_final: 0.7038 (ptp90) REVERT: A 142 TYR cc_start: 0.8371 (m-10) cc_final: 0.7835 (m-80) REVERT: A 368 GLU cc_start: 0.7694 (tt0) cc_final: 0.7324 (mm-30) REVERT: A 552 MET cc_start: 0.8850 (mtp) cc_final: 0.8398 (mtp) REVERT: A 663 PHE cc_start: 0.8503 (m-80) cc_final: 0.8248 (m-10) REVERT: B 32 MET cc_start: 0.7030 (pmm) cc_final: 0.6751 (pmm) REVERT: B 76 ASP cc_start: 0.8559 (p0) cc_final: 0.8139 (p0) REVERT: B 324 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7634 (t-170) REVERT: C 78 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8656 (mmmm) REVERT: C 202 MET cc_start: 0.6902 (mmt) cc_final: 0.6364 (mmt) REVERT: E 50 MET cc_start: 0.7308 (tpp) cc_final: 0.7099 (mmp) REVERT: E 102 THR cc_start: 0.8520 (m) cc_final: 0.8164 (t) outliers start: 69 outliers final: 55 residues processed: 214 average time/residue: 0.2022 time to fit residues: 66.6002 Evaluate side-chains 198 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 352 ILE Chi-restraints excluded: chain A residue 372 MET 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 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 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 258 VAL 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 324 HIS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 55 LEU 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 186 THR Chi-restraints excluded: chain D residue 205 TYR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 180 ASN ** 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 = 0.3797 r_free = 0.3797 target = 0.117875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090427 restraints weight = 57676.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093331 restraints weight = 23223.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095204 restraints weight = 12778.033| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3346 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= 0.134 Angle : 0.656 7.836 18008 Z= 0.339 Chirality : 0.044 0.155 1978 Planarity : 0.004 0.037 2374 Dihedral : 5.889 57.083 1834 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.59 % Allowed : 20.96 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.20), residues: 1643 helix: 0.38 (0.28), residues: 354 sheet: -3.08 (0.22), residues: 415 loop : -3.05 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.020 0.001 TYR C 157 ARG 0.004 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 386) hydrogen bonds : angle 4.92408 ( 1029) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.33664 ( 2) covalent geometry : bond 0.00294 (13255) covalent geometry : angle 0.65605 (18006) *********************** 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 227 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8380 (m-10) cc_final: 0.7800 (m-80) REVERT: A 368 GLU cc_start: 0.7549 (tt0) cc_final: 0.7312 (mm-30) REVERT: A 552 MET cc_start: 0.8825 (mtp) cc_final: 0.8581 (mtp) REVERT: A 663 PHE cc_start: 0.8443 (m-80) cc_final: 0.8207 (m-10) REVERT: A 776 TRP cc_start: 0.8070 (t60) cc_final: 0.7744 (t60) REVERT: B 32 MET cc_start: 0.7087 (pmm) cc_final: 0.6629 (pmm) REVERT: B 76 ASP cc_start: 0.8383 (p0) cc_final: 0.8071 (p0) REVERT: B 171 LEU cc_start: 0.8510 (mp) cc_final: 0.8118 (mt) REVERT: B 324 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7611 (t-170) REVERT: C 57 ILE cc_start: 0.8943 (mm) cc_final: 0.8629 (mt) REVERT: C 202 MET cc_start: 0.6515 (mmt) cc_final: 0.6181 (mmt) REVERT: D 34 GLU cc_start: 0.7757 (pm20) cc_final: 0.7385 (mp0) REVERT: D 56 GLU cc_start: 0.8132 (tp30) cc_final: 0.7887 (tp30) REVERT: D 84 ASP cc_start: 0.8093 (t0) cc_final: 0.7816 (t70) REVERT: D 114 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8761 (tp) REVERT: E 50 MET cc_start: 0.7155 (tpp) cc_final: 0.6920 (mmp) REVERT: E 67 PRO cc_start: 0.8947 (Cg_endo) cc_final: 0.8704 (Cg_exo) outliers start: 59 outliers final: 44 residues processed: 215 average time/residue: 0.2219 time to fit residues: 74.5959 Evaluate side-chains 200 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 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 511 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 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 153 SER Chi-restraints excluded: chain B residue 156 VAL 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 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 324 HIS 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 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 187 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 21 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086325 restraints weight = 68589.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088974 restraints weight = 25634.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091775 restraints weight = 14514.261| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13256 Z= 0.248 Angle : 0.736 10.837 18008 Z= 0.382 Chirality : 0.046 0.180 1978 Planarity : 0.005 0.040 2374 Dihedral : 6.283 55.659 1834 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 5.68 % Allowed : 20.74 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.19), residues: 1643 helix: 0.11 (0.27), residues: 353 sheet: -3.09 (0.22), residues: 418 loop : -3.09 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 191 HIS 0.005 0.001 HIS A 677 PHE 0.027 0.002 PHE A 478 TYR 0.025 0.002 TYR A 454 ARG 0.004 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 386) hydrogen bonds : angle 5.21019 ( 1029) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.60810 ( 2) covalent geometry : bond 0.00549 (13255) covalent geometry : angle 0.73615 (18006) *********************** 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 227 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 151 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7356 (ptp90) cc_final: 0.6802 (ptp90) REVERT: A 142 TYR cc_start: 0.8313 (m-10) cc_final: 0.7721 (m-80) REVERT: A 259 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8488 (m-40) REVERT: A 368 GLU cc_start: 0.7579 (tt0) cc_final: 0.7339 (mm-30) REVERT: A 552 MET cc_start: 0.8902 (mtp) cc_final: 0.8660 (mtp) REVERT: A 663 PHE cc_start: 0.8474 (m-80) cc_final: 0.8204 (m-10) REVERT: A 729 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: A 776 TRP cc_start: 0.8168 (t60) cc_final: 0.7674 (t60) REVERT: B 32 MET cc_start: 0.7448 (pmm) cc_final: 0.7025 (pmm) REVERT: B 76 ASP cc_start: 0.8555 (p0) cc_final: 0.8179 (p0) REVERT: B 97 LEU cc_start: 0.8806 (mt) cc_final: 0.8500 (mt) REVERT: B 138 ASP cc_start: 0.8171 (p0) cc_final: 0.7882 (p0) REVERT: B 171 LEU cc_start: 0.8490 (mp) cc_final: 0.8117 (mt) REVERT: B 261 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 324 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7656 (t-170) REVERT: C 129 TYR cc_start: 0.6335 (m-10) cc_final: 0.5883 (m-80) REVERT: C 202 MET cc_start: 0.6646 (mmt) cc_final: 0.6280 (mmt) REVERT: D 84 ASP cc_start: 0.8243 (t0) cc_final: 0.8020 (t70) REVERT: E 50 MET cc_start: 0.7306 (tpp) cc_final: 0.7091 (mmp) outliers start: 76 outliers final: 62 residues processed: 213 average time/residue: 0.2012 time to fit residues: 66.6800 Evaluate side-chains 209 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 259 ASN 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 382 VAL 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 555 HIS Chi-restraints excluded: chain A residue 600 THR 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 729 TYR 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 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 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 324 HIS 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 369 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 35 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 0.0370 chunk 161 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 153 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 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 = 0.3794 r_free = 0.3794 target = 0.117658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090158 restraints weight = 89322.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093226 restraints weight = 31956.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094448 restraints weight = 18108.923| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13256 Z= 0.134 Angle : 0.663 9.399 18008 Z= 0.341 Chirality : 0.044 0.169 1978 Planarity : 0.004 0.035 2374 Dihedral : 5.843 54.408 1834 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.02 % Allowed : 21.25 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.20), residues: 1643 helix: 0.41 (0.28), residues: 353 sheet: -3.02 (0.22), residues: 427 loop : -2.95 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.020 0.001 PHE A 478 TYR 0.019 0.001 TYR A 504 ARG 0.004 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 386) hydrogen bonds : angle 4.85801 ( 1029) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.35935 ( 2) covalent geometry : bond 0.00297 (13255) covalent geometry : angle 0.66342 (18006) *********************** 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 233 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.9104 (p0) cc_final: 0.8825 (p0) REVERT: A 115 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8796 (mm-30) REVERT: A 142 TYR cc_start: 0.8262 (m-10) cc_final: 0.7644 (m-80) REVERT: A 272 GLU cc_start: 0.8182 (tp30) cc_final: 0.7828 (tp30) REVERT: A 368 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: A 663 PHE cc_start: 0.8467 (m-80) cc_final: 0.8190 (m-10) REVERT: A 729 TYR cc_start: 0.6246 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: A 776 TRP cc_start: 0.8136 (t60) cc_final: 0.7692 (t60) REVERT: B 32 MET cc_start: 0.7373 (pmm) cc_final: 0.6783 (pmm) REVERT: B 76 ASP cc_start: 0.8335 (p0) cc_final: 0.8037 (p0) REVERT: B 97 LEU cc_start: 0.8797 (mt) cc_final: 0.8521 (mt) REVERT: B 171 LEU cc_start: 0.8508 (mp) cc_final: 0.8147 (mt) REVERT: B 249 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 261 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8293 (tp) REVERT: B 324 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7528 (t-170) REVERT: C 57 ILE cc_start: 0.8935 (mm) cc_final: 0.8634 (mt) REVERT: C 129 TYR cc_start: 0.6365 (m-10) cc_final: 0.6050 (m-80) REVERT: C 202 MET cc_start: 0.6507 (mmt) cc_final: 0.6253 (mmt) REVERT: C 205 ILE cc_start: 0.8751 (mm) cc_final: 0.8442 (mt) REVERT: D 109 MET cc_start: 0.7873 (mtt) cc_final: 0.7433 (mtt) REVERT: D 114 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8807 (tp) REVERT: E 50 MET cc_start: 0.7185 (tpp) cc_final: 0.6956 (mmp) REVERT: E 67 PRO cc_start: 0.8902 (Cg_endo) cc_final: 0.8673 (Cg_exo) outliers start: 67 outliers final: 54 residues processed: 220 average time/residue: 0.1880 time to fit residues: 65.0308 Evaluate side-chains 207 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 290 ILE 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 368 GLU 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 555 HIS Chi-restraints excluded: chain A residue 600 THR 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 729 TYR 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 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 324 HIS 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 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 D residue 208 THR Chi-restraints excluded: chain D residue 211 THR 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 F residue 1274 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087989 restraints weight = 75138.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090711 restraints weight = 26899.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093223 restraints weight = 15366.766| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13256 Z= 0.208 Angle : 0.715 9.839 18008 Z= 0.372 Chirality : 0.046 0.193 1978 Planarity : 0.004 0.039 2374 Dihedral : 5.996 53.883 1832 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.27 % Favored : 85.73 % Rotamer: Outliers : 5.24 % Allowed : 22.20 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.20), residues: 1643 helix: 0.25 (0.27), residues: 355 sheet: -2.95 (0.23), residues: 414 loop : -2.98 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 191 HIS 0.004 0.001 HIS A 677 PHE 0.027 0.002 PHE A 478 TYR 0.032 0.002 TYR C 157 ARG 0.004 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 386) hydrogen bonds : angle 5.00598 ( 1029) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.44061 ( 2) covalent geometry : bond 0.00463 (13255) covalent geometry : angle 0.71549 (18006) *********************** 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 222 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 152 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8329 (m-10) cc_final: 0.7701 (m-80) REVERT: A 368 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: A 653 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7724 (p90) REVERT: A 729 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: A 776 TRP cc_start: 0.8250 (t60) cc_final: 0.7735 (t60) REVERT: B 32 MET cc_start: 0.7441 (pmm) cc_final: 0.6763 (pmm) REVERT: B 76 ASP cc_start: 0.8491 (p0) cc_final: 0.8130 (p0) REVERT: B 97 LEU cc_start: 0.8903 (mt) cc_final: 0.8596 (mt) REVERT: B 171 LEU cc_start: 0.8527 (mp) cc_final: 0.8180 (mt) REVERT: B 261 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8307 (tp) REVERT: C 57 ILE cc_start: 0.8985 (mm) cc_final: 0.8671 (mt) REVERT: C 205 ILE cc_start: 0.8684 (mm) cc_final: 0.8377 (mt) REVERT: D 34 GLU cc_start: 0.8177 (pm20) cc_final: 0.7961 (mp0) REVERT: E 50 MET cc_start: 0.7285 (tpp) cc_final: 0.7053 (mmp) outliers start: 70 outliers final: 63 residues processed: 209 average time/residue: 0.1928 time to fit residues: 63.4835 Evaluate side-chains 212 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 ILE 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 368 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 474 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 555 HIS Chi-restraints excluded: chain A residue 600 THR 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 653 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 729 TYR 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 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 331 VAL 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 D residue 27 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 VAL 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 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 F residue 1274 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 60 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 129 optimal weight: 0.0670 chunk 76 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088375 restraints weight = 93314.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091279 restraints weight = 34241.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092578 restraints weight = 18914.632| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13256 Z= 0.189 Angle : 0.711 9.499 18008 Z= 0.369 Chirality : 0.046 0.217 1978 Planarity : 0.004 0.037 2374 Dihedral : 5.965 52.847 1832 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 5.60 % Allowed : 21.98 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.20), residues: 1643 helix: 0.27 (0.27), residues: 354 sheet: -2.91 (0.23), residues: 416 loop : -2.95 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 PHE 0.025 0.002 PHE A 478 TYR 0.029 0.002 TYR C 157 ARG 0.004 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 386) hydrogen bonds : angle 4.98385 ( 1029) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.42097 ( 2) covalent geometry : bond 0.00419 (13255) covalent geometry : angle 0.71067 (18006) *********************** 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 227 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 152 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8250 (m-10) cc_final: 0.7635 (m-80) REVERT: A 368 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: A 653 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7745 (p90) REVERT: A 729 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: A 776 TRP cc_start: 0.8216 (t60) cc_final: 0.7679 (t60) REVERT: B 32 MET cc_start: 0.7574 (pmm) cc_final: 0.6910 (pmm) REVERT: B 76 ASP cc_start: 0.8484 (p0) cc_final: 0.8144 (p0) REVERT: B 97 LEU cc_start: 0.8852 (mt) cc_final: 0.8561 (mt) REVERT: B 171 LEU cc_start: 0.8551 (mp) cc_final: 0.8221 (mt) REVERT: B 261 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8366 (tp) REVERT: C 57 ILE cc_start: 0.8966 (mm) cc_final: 0.8642 (mt) REVERT: C 129 TYR cc_start: 0.6351 (m-10) cc_final: 0.5857 (m-80) REVERT: C 205 ILE cc_start: 0.8666 (mm) cc_final: 0.8413 (mt) REVERT: D 114 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8835 (tp) REVERT: E 33 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7853 (p0) REVERT: E 50 MET cc_start: 0.7282 (tpp) cc_final: 0.7051 (mmp) outliers start: 75 outliers final: 65 residues processed: 214 average time/residue: 0.1933 time to fit residues: 64.6050 Evaluate side-chains 214 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 143 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 156 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 ILE 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 368 GLU 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 474 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 555 HIS Chi-restraints excluded: chain A residue 600 THR 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 653 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 729 TYR 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 95 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 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 331 VAL 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 D residue 27 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 51 THR 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 102 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 8 optimal weight: 0.0370 chunk 159 optimal weight: 8.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** 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 = 0.3748 r_free = 0.3748 target = 0.114521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086958 restraints weight = 84650.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089803 restraints weight = 31036.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090793 restraints weight = 18537.516| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13256 Z= 0.240 Angle : 0.762 11.676 18008 Z= 0.395 Chirality : 0.048 0.241 1978 Planarity : 0.005 0.051 2374 Dihedral : 6.152 52.589 1832 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 5.68 % Allowed : 21.91 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.20), residues: 1643 helix: 0.13 (0.27), residues: 354 sheet: -2.95 (0.23), residues: 409 loop : -2.98 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 191 HIS 0.005 0.001 HIS A 677 PHE 0.027 0.002 PHE A 478 TYR 0.034 0.002 TYR C 197 ARG 0.014 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 386) hydrogen bonds : angle 5.18387 ( 1029) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.44519 ( 2) covalent geometry : bond 0.00534 (13255) covalent geometry : angle 0.76215 (18006) ********************** 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 223 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 147 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8713 (mm-30) REVERT: A 142 TYR cc_start: 0.8258 (m-10) cc_final: 0.7659 (m-80) REVERT: A 368 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: A 653 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7669 (p90) REVERT: A 729 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: A 776 TRP cc_start: 0.8246 (t60) cc_final: 0.7744 (t60) REVERT: B 32 MET cc_start: 0.7644 (pmm) cc_final: 0.7023 (pmm) REVERT: B 76 ASP cc_start: 0.8551 (p0) cc_final: 0.8177 (p0) REVERT: B 97 LEU cc_start: 0.8889 (mt) cc_final: 0.8589 (mt) REVERT: B 171 LEU cc_start: 0.8631 (mp) cc_final: 0.8314 (mt) REVERT: B 261 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 324 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7556 (t-170) REVERT: C 57 ILE cc_start: 0.9026 (mm) cc_final: 0.8718 (mt) REVERT: C 129 TYR cc_start: 0.6318 (m-10) cc_final: 0.5770 (m-80) REVERT: C 157 TYR cc_start: 0.4193 (m-80) cc_final: 0.3262 (m-80) REVERT: C 205 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8317 (mt) REVERT: D 74 ASP cc_start: 0.8181 (t0) cc_final: 0.7940 (t0) REVERT: E 50 MET cc_start: 0.7414 (tpp) cc_final: 0.7180 (mmp) outliers start: 76 outliers final: 65 residues processed: 209 average time/residue: 0.2026 time to fit residues: 65.4853 Evaluate side-chains 216 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 145 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 ILE 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 368 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 474 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 555 HIS Chi-restraints excluded: chain A residue 600 THR 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 653 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 729 TYR 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 95 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 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 324 HIS Chi-restraints excluded: chain B residue 329 SER 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 369 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 ILE 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 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 THR 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 F residue 1274 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 78 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 92 optimal weight: 10.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.120059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093299 restraints weight = 94713.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097362 restraints weight = 34448.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097972 restraints weight = 17977.584| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 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 = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13256 Z= 0.125 Angle : 0.697 10.231 18008 Z= 0.356 Chirality : 0.046 0.211 1978 Planarity : 0.004 0.053 2374 Dihedral : 5.641 51.521 1832 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.78 % Allowed : 23.87 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.20), residues: 1643 helix: 0.42 (0.27), residues: 354 sheet: -2.77 (0.23), residues: 412 loop : -2.80 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 191 HIS 0.005 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.030 0.001 TYR C 157 ARG 0.013 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 386) hydrogen bonds : angle 4.85807 ( 1029) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.23074 ( 2) covalent geometry : bond 0.00278 (13255) covalent geometry : angle 0.69660 (18006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.52 seconds wall clock time: 73 minutes 4.78 seconds (4384.78 seconds total)