Starting phenix.real_space_refine on Mon Dec 30 11:38:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqb_40701/12_2024/8sqb_40701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqb_40701/12_2024/8sqb_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_40701/12_2024/8sqb_40701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqb_40701/12_2024/8sqb_40701.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqb_40701/12_2024/8sqb_40701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqb_40701/12_2024/8sqb_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-5532/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: 8.44, per 1000 atoms: 0.65 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: 3.41 Conformation dependent library (CDL) restraints added in 2.0 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: 1.42 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: 4.22 Time building geometry restraints manager: 3.92 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: 0.010 Normalize map: mean=0, sd=1: 1.030 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.990 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- 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 13255 Z= 0.519 Angle : 0.840 12.652 18006 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 *********************** 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 : 1.535 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: 0.2728 time to fit residues: 81.4845 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 : 1.889 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 13255 Z= 0.255 Angle : 0.716 8.349 18006 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 *********************** 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 : 1.548 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 142 TYR cc_start: 0.8706 (m-10) cc_final: 0.8230 (m-80) REVERT: A 147 TYR cc_start: 0.8764 (m-80) cc_final: 0.8539 (m-80) REVERT: A 325 MET cc_start: 0.7934 (ptp) cc_final: 0.6865 (ppp) REVERT: A 663 PHE cc_start: 0.7689 (m-80) cc_final: 0.7418 (m-80) REVERT: A 797 ASP cc_start: 0.7414 (m-30) cc_final: 0.7176 (m-30) REVERT: A 801 GLN cc_start: 0.7685 (mt0) cc_final: 0.7435 (mp10) REVERT: B 32 MET cc_start: 0.6990 (pmm) cc_final: 0.6404 (pmm) REVERT: B 221 MET cc_start: 0.8484 (mtp) cc_final: 0.8268 (mtt) REVERT: B 278 MET cc_start: 0.6408 (mmt) cc_final: 0.5948 (tpp) REVERT: C 78 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8141 (mmmm) REVERT: C 127 LYS cc_start: 0.6870 (mmtt) cc_final: 0.6532 (mppt) REVERT: C 133 GLN cc_start: 0.8258 (tp-100) cc_final: 0.8007 (tp40) REVERT: C 202 MET cc_start: 0.6495 (mmt) cc_final: 0.6105 (mmt) REVERT: D 52 ILE cc_start: 0.7454 (mt) cc_final: 0.7153 (mt) REVERT: D 53 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8695 (t) REVERT: D 109 MET cc_start: 0.7206 (mmt) cc_final: 0.6684 (mtt) REVERT: D 111 MET cc_start: 0.8528 (tpp) cc_final: 0.8070 (tpp) REVERT: D 191 TRP cc_start: 0.8651 (m-10) cc_final: 0.8240 (m-10) REVERT: D 199 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7078 (tm-30) REVERT: D 201 MET cc_start: 0.7367 (ttp) cc_final: 0.6603 (mtp) REVERT: E 33 ASN cc_start: 0.7912 (p0) cc_final: 0.7329 (p0) REVERT: E 36 ASN cc_start: 0.8652 (t0) cc_final: 0.8018 (t0) REVERT: E 50 MET cc_start: 0.6972 (mmt) cc_final: 0.6686 (tpp) REVERT: E 87 THR cc_start: 0.8244 (t) cc_final: 0.8033 (p) REVERT: E 101 LEU cc_start: 0.7799 (tt) cc_final: 0.7550 (tt) outliers start: 47 outliers final: 25 residues processed: 213 average time/residue: 0.2375 time to fit residues: 74.9529 Evaluate side-chains 176 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 82 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13255 Z= 0.300 Angle : 0.704 7.624 18006 Z= 0.367 Chirality : 0.046 0.176 1978 Planarity : 0.004 0.040 2374 Dihedral : 6.376 58.798 1835 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.72 % Favored : 86.28 % Rotamer: Outliers : 4.22 % Allowed : 17.61 % Favored : 78.17 % 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: -3.93 (0.19), residues: 1643 helix: -0.08 (0.27), residues: 352 sheet: -3.48 (0.22), residues: 397 loop : -3.36 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 228 HIS 0.005 0.001 HIS A 677 PHE 0.023 0.002 PHE A 478 TYR 0.023 0.002 TYR A 454 ARG 0.005 0.001 ARG A 367 *********************** 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 220 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 1.556 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: 0.8707 (m-10) cc_final: 0.8289 (m-80) REVERT: A 147 TYR cc_start: 0.8725 (m-80) cc_final: 0.8494 (m-80) REVERT: A 325 MET cc_start: 0.7929 (ptp) cc_final: 0.6867 (ppp) REVERT: A 368 GLU cc_start: 0.7668 (tt0) cc_final: 0.7241 (tt0) REVERT: A 470 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 663 PHE cc_start: 0.7909 (m-80) cc_final: 0.7617 (m-80) REVERT: A 797 ASP cc_start: 0.7390 (m-30) cc_final: 0.7123 (m-30) REVERT: A 801 GLN cc_start: 0.7705 (mt0) cc_final: 0.7439 (mp10) REVERT: B 32 MET cc_start: 0.7227 (pmm) cc_final: 0.6704 (pmm) REVERT: B 221 MET cc_start: 0.8507 (mtp) cc_final: 0.8243 (mtt) REVERT: B 278 MET cc_start: 0.6462 (mmt) cc_final: 0.5940 (tpp) REVERT: C 39 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7542 (mm-30) REVERT: C 78 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8233 (mmtp) REVERT: C 109 GLU cc_start: 0.7940 (tt0) cc_final: 0.7734 (tt0) REVERT: C 127 LYS cc_start: 0.6745 (mmtt) cc_final: 0.6444 (mppt) REVERT: C 148 TRP cc_start: 0.6616 (m100) cc_final: 0.6395 (m100) REVERT: C 202 MET cc_start: 0.6687 (mmt) cc_final: 0.6421 (mmt) REVERT: D 109 MET cc_start: 0.7264 (mmt) cc_final: 0.6837 (mtt) REVERT: D 111 MET cc_start: 0.8321 (tpp) cc_final: 0.8055 (tpp) REVERT: D 191 TRP cc_start: 0.8655 (m-10) cc_final: 0.8394 (m-10) REVERT: E 33 ASN cc_start: 0.7929 (p0) cc_final: 0.7299 (p0) outliers start: 54 outliers final: 44 residues processed: 212 average time/residue: 0.2284 time to fit residues: 73.9541 Evaluate side-chains 194 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 408 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13255 Z= 0.235 Angle : 0.658 7.615 18006 Z= 0.341 Chirality : 0.045 0.191 1978 Planarity : 0.004 0.037 2374 Dihedral : 6.097 58.176 1835 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 4.88 % Allowed : 19.21 % Favored : 75.91 % 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: -3.63 (0.19), residues: 1643 helix: 0.29 (0.27), residues: 353 sheet: -3.28 (0.22), residues: 404 loop : -3.21 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.029 0.002 TYR C 157 ARG 0.005 0.000 ARG C 83 *********************** 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 233 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8732 (m-10) cc_final: 0.8292 (m-80) REVERT: A 147 TYR cc_start: 0.8754 (m-80) cc_final: 0.8511 (m-80) REVERT: A 325 MET cc_start: 0.7973 (ptp) cc_final: 0.6845 (ppp) REVERT: A 582 ASP cc_start: 0.8889 (t0) cc_final: 0.8668 (t0) REVERT: A 663 PHE cc_start: 0.7940 (m-80) cc_final: 0.7677 (m-10) REVERT: A 776 TRP cc_start: 0.6433 (t60) cc_final: 0.6228 (t-100) REVERT: A 797 ASP cc_start: 0.7356 (m-30) cc_final: 0.7137 (m-30) REVERT: A 801 GLN cc_start: 0.7733 (mt0) cc_final: 0.7114 (mt0) REVERT: B 27 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8139 (mp0) REVERT: B 32 MET cc_start: 0.7351 (pmm) cc_final: 0.6956 (pmm) REVERT: B 171 LEU cc_start: 0.8253 (mp) cc_final: 0.7984 (mt) REVERT: B 221 MET cc_start: 0.8515 (mtp) cc_final: 0.8290 (mtt) REVERT: B 261 LEU cc_start: 0.8537 (mp) cc_final: 0.8261 (mt) REVERT: B 278 MET cc_start: 0.6742 (mmt) cc_final: 0.6138 (tpp) REVERT: C 127 LYS cc_start: 0.6798 (mmtt) cc_final: 0.6493 (mppt) REVERT: C 148 TRP cc_start: 0.6761 (m100) cc_final: 0.6367 (m100) REVERT: C 202 MET cc_start: 0.6722 (mmt) cc_final: 0.6427 (mmt) REVERT: D 109 MET cc_start: 0.7197 (mmt) cc_final: 0.6768 (mtt) REVERT: D 191 TRP cc_start: 0.8629 (m-10) cc_final: 0.8374 (m-10) REVERT: D 218 MET cc_start: 0.8080 (mtp) cc_final: 0.7782 (mtt) REVERT: E 36 ASN cc_start: 0.8595 (t0) cc_final: 0.7922 (t0) REVERT: E 76 VAL cc_start: 0.7124 (OUTLIER) cc_final: 0.6823 (p) REVERT: E 102 THR cc_start: 0.7979 (m) cc_final: 0.7603 (t) REVERT: E 103 ASN cc_start: 0.7956 (m110) cc_final: 0.7710 (m-40) outliers start: 63 outliers final: 47 residues processed: 222 average time/residue: 0.2213 time to fit residues: 75.3540 Evaluate side-chains 197 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 382 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 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 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 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 124 LEU 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 185 TYR 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 68 PHE Chi-restraints excluded: chain E residue 76 VAL 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 132 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 178 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13255 Z= 0.185 Angle : 0.632 7.878 18006 Z= 0.327 Chirality : 0.044 0.191 1978 Planarity : 0.004 0.037 2374 Dihedral : 5.788 56.434 1835 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 5.31 % Allowed : 19.72 % Favored : 74.96 % 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 (0.19), residues: 1643 helix: 0.40 (0.27), residues: 354 sheet: -3.04 (0.22), residues: 405 loop : -3.06 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.023 0.001 PHE A 478 TYR 0.019 0.001 TYR C 157 ARG 0.005 0.000 ARG C 83 *********************** 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 237 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 168 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.9007 (ptp) cc_final: 0.8630 (ptp) REVERT: A 115 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8866 (mm-30) REVERT: A 142 TYR cc_start: 0.8736 (m-10) cc_final: 0.8268 (m-80) REVERT: A 147 TYR cc_start: 0.8810 (m-80) cc_final: 0.8561 (m-80) REVERT: A 192 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8340 (pp20) REVERT: A 325 MET cc_start: 0.7939 (ptp) cc_final: 0.6884 (ppp) REVERT: A 582 ASP cc_start: 0.8874 (t0) cc_final: 0.8659 (t0) REVERT: A 663 PHE cc_start: 0.7916 (m-80) cc_final: 0.7697 (m-10) REVERT: A 801 GLN cc_start: 0.7752 (mt0) cc_final: 0.7486 (mp10) REVERT: B 27 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8167 (mp0) REVERT: B 32 MET cc_start: 0.7335 (pmm) cc_final: 0.6926 (pmm) REVERT: B 76 ASP cc_start: 0.7923 (p0) cc_final: 0.7551 (p0) REVERT: B 127 GLU cc_start: 0.8485 (tp30) cc_final: 0.8208 (tp30) REVERT: B 171 LEU cc_start: 0.8271 (mp) cc_final: 0.8040 (mt) REVERT: B 221 MET cc_start: 0.8525 (mtp) cc_final: 0.8289 (mtt) REVERT: B 261 LEU cc_start: 0.8565 (mp) cc_final: 0.8258 (tp) REVERT: B 278 MET cc_start: 0.6702 (mmt) cc_final: 0.6153 (tpp) REVERT: C 43 GLU cc_start: 0.9031 (pt0) cc_final: 0.8556 (pm20) REVERT: C 127 LYS cc_start: 0.6716 (mmtt) cc_final: 0.6467 (mppt) REVERT: C 148 TRP cc_start: 0.6859 (m100) cc_final: 0.6260 (m100) REVERT: D 49 ARG cc_start: 0.8302 (ptt-90) cc_final: 0.8075 (ptp-110) REVERT: D 80 TYR cc_start: 0.8721 (t80) cc_final: 0.8343 (t80) REVERT: D 84 ASP cc_start: 0.8506 (t0) cc_final: 0.7811 (t70) REVERT: D 109 MET cc_start: 0.7080 (mmt) cc_final: 0.6716 (mtt) REVERT: D 111 MET cc_start: 0.8457 (tpp) cc_final: 0.8193 (tpp) REVERT: D 191 TRP cc_start: 0.8584 (m-10) cc_final: 0.8242 (m-10) REVERT: E 36 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7940 (t0) REVERT: E 76 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6714 (p) REVERT: E 96 ASN cc_start: 0.8450 (t0) cc_final: 0.8087 (t0) REVERT: E 101 LEU cc_start: 0.7685 (tt) cc_final: 0.7466 (tt) outliers start: 69 outliers final: 53 residues processed: 224 average time/residue: 0.2228 time to fit residues: 77.4019 Evaluate side-chains 214 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 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 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 744 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 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 189 MET 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 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 C residue 124 LEU 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 127 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 TYR 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 36 ASN Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 76 VAL 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 53 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 13 optimal weight: 0.0030 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 overall best weight: 0.4768 ------------------------------------------------------------------------------- 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** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13255 Z= 0.160 Angle : 0.627 9.207 18006 Z= 0.321 Chirality : 0.044 0.203 1978 Planarity : 0.003 0.036 2374 Dihedral : 5.496 55.563 1834 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.15 % Allowed : 21.11 % Favored : 74.75 % 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: -3.16 (0.20), residues: 1643 helix: 0.57 (0.28), residues: 354 sheet: -2.91 (0.22), residues: 423 loop : -2.90 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.026 0.001 TYR C 197 ARG 0.004 0.000 ARG C 158 *********************** 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 241 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8719 (m-10) cc_final: 0.8249 (m-80) REVERT: A 147 TYR cc_start: 0.8802 (m-80) cc_final: 0.8539 (m-80) REVERT: A 191 ASP cc_start: 0.9119 (p0) cc_final: 0.8032 (t0) REVERT: A 192 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: A 325 MET cc_start: 0.7848 (ptp) cc_final: 0.6839 (ppp) REVERT: A 368 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 545 MET cc_start: 0.7322 (tpp) cc_final: 0.7047 (tpp) REVERT: A 546 TRP cc_start: 0.6350 (m100) cc_final: 0.5899 (m-10) REVERT: A 582 ASP cc_start: 0.8839 (t0) cc_final: 0.8587 (t0) REVERT: A 663 PHE cc_start: 0.7903 (m-80) cc_final: 0.7696 (m-10) REVERT: A 801 GLN cc_start: 0.7750 (mt0) cc_final: 0.7473 (mp10) REVERT: B 27 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8267 (mp0) REVERT: B 76 ASP cc_start: 0.7790 (p0) cc_final: 0.7505 (p0) REVERT: B 127 GLU cc_start: 0.8475 (tp30) cc_final: 0.8121 (tp30) REVERT: B 171 LEU cc_start: 0.8233 (mp) cc_final: 0.8014 (mt) REVERT: B 221 MET cc_start: 0.8549 (mtp) cc_final: 0.8311 (mtt) REVERT: B 248 ASP cc_start: 0.7289 (m-30) cc_final: 0.6398 (p0) REVERT: B 249 THR cc_start: 0.6759 (OUTLIER) cc_final: 0.6434 (p) REVERT: B 261 LEU cc_start: 0.8589 (mp) cc_final: 0.8268 (tp) REVERT: B 278 MET cc_start: 0.6696 (mmt) cc_final: 0.6144 (tpp) REVERT: C 43 GLU cc_start: 0.9021 (pt0) cc_final: 0.8579 (pm20) REVERT: C 127 LYS cc_start: 0.6707 (mmtt) cc_final: 0.6480 (mppt) REVERT: C 148 TRP cc_start: 0.6846 (m100) cc_final: 0.6459 (m100) REVERT: C 157 TYR cc_start: 0.2490 (m-80) cc_final: 0.1803 (m-80) REVERT: C 186 LYS cc_start: 0.5676 (tppp) cc_final: 0.5390 (ttpt) REVERT: D 84 ASP cc_start: 0.8546 (t0) cc_final: 0.7757 (t70) REVERT: D 109 MET cc_start: 0.7253 (mmt) cc_final: 0.7002 (mtt) REVERT: D 191 TRP cc_start: 0.8462 (m-10) cc_final: 0.8074 (m-10) REVERT: E 36 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8025 (t0) REVERT: E 76 VAL cc_start: 0.7042 (OUTLIER) cc_final: 0.6590 (p) REVERT: E 96 ASN cc_start: 0.8493 (t0) cc_final: 0.8111 (t0) REVERT: E 102 THR cc_start: 0.8161 (m) cc_final: 0.7883 (t) outliers start: 53 outliers final: 43 residues processed: 228 average time/residue: 0.2199 time to fit residues: 77.2416 Evaluate side-chains 209 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR 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 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain 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 153 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 249 THR 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 306 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 124 LEU 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 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 76 VAL 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 152 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** E 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13255 Z= 0.196 Angle : 0.629 8.977 18006 Z= 0.324 Chirality : 0.044 0.207 1978 Planarity : 0.004 0.036 2374 Dihedral : 5.577 55.085 1834 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 5.09 % Allowed : 20.96 % Favored : 73.94 % 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: -3.10 (0.20), residues: 1643 helix: 0.56 (0.28), residues: 356 sheet: -2.83 (0.23), residues: 412 loop : -2.87 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.025 0.001 PHE A 478 TYR 0.039 0.002 TYR C 197 ARG 0.005 0.000 ARG C 83 *********************** 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 231 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 165 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8726 (m-10) cc_final: 0.8257 (m-80) REVERT: A 147 TYR cc_start: 0.8832 (m-80) cc_final: 0.8550 (m-80) REVERT: A 191 ASP cc_start: 0.9125 (p0) cc_final: 0.8087 (t0) REVERT: A 192 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8202 (pp20) REVERT: A 325 MET cc_start: 0.7873 (ptp) cc_final: 0.6866 (ppp) REVERT: A 368 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7546 (mm-30) REVERT: A 408 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8503 (p) REVERT: A 552 MET cc_start: 0.8439 (mtp) cc_final: 0.8191 (mtp) REVERT: A 582 ASP cc_start: 0.8831 (t0) cc_final: 0.8569 (t0) REVERT: A 663 PHE cc_start: 0.7957 (m-80) cc_final: 0.7746 (m-10) REVERT: A 801 GLN cc_start: 0.7775 (mt0) cc_final: 0.7134 (mt0) REVERT: B 27 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8255 (mp0) REVERT: B 76 ASP cc_start: 0.7807 (p0) cc_final: 0.7547 (p0) REVERT: B 221 MET cc_start: 0.8566 (mtp) cc_final: 0.8326 (mtt) REVERT: B 248 ASP cc_start: 0.7059 (m-30) cc_final: 0.6072 (p0) REVERT: B 249 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6540 (p) REVERT: B 261 LEU cc_start: 0.8624 (mp) cc_final: 0.8282 (tp) REVERT: B 278 MET cc_start: 0.6673 (mmt) cc_final: 0.6135 (tpp) REVERT: C 43 GLU cc_start: 0.9023 (pt0) cc_final: 0.8572 (pm20) REVERT: C 127 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6283 (mppt) REVERT: C 148 TRP cc_start: 0.6941 (m100) cc_final: 0.6514 (m100) REVERT: D 84 ASP cc_start: 0.8562 (t0) cc_final: 0.7808 (t70) REVERT: D 109 MET cc_start: 0.7252 (mmt) cc_final: 0.7012 (mtt) REVERT: D 191 TRP cc_start: 0.8559 (m-10) cc_final: 0.8219 (m-10) REVERT: E 36 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8156 (t0) REVERT: E 76 VAL cc_start: 0.7022 (OUTLIER) cc_final: 0.6732 (p) REVERT: E 96 ASN cc_start: 0.8509 (t0) cc_final: 0.8104 (t0) outliers start: 66 outliers final: 52 residues processed: 219 average time/residue: 0.2139 time to fit residues: 73.1925 Evaluate side-chains 216 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 408 SER 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 621 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 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 189 MET 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 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 306 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 101 LEU 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 63 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 165 HIS ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13255 Z= 0.453 Angle : 0.798 12.550 18006 Z= 0.417 Chirality : 0.049 0.259 1978 Planarity : 0.005 0.053 2374 Dihedral : 6.408 54.298 1832 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.40 % Favored : 83.60 % Rotamer: Outliers : 5.17 % Allowed : 21.18 % Favored : 73.65 % 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: -3.48 (0.20), residues: 1643 helix: 0.13 (0.27), residues: 351 sheet: -3.05 (0.23), residues: 408 loop : -3.05 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 228 HIS 0.007 0.002 HIS A 677 PHE 0.031 0.003 PHE A 478 TYR 0.054 0.003 TYR C 197 ARG 0.004 0.001 ARG A 547 *********************** 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 218 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7383 (ptp90) cc_final: 0.6888 (ptp90) REVERT: A 142 TYR cc_start: 0.8687 (m-10) cc_final: 0.8234 (m-80) REVERT: A 147 TYR cc_start: 0.8782 (m-80) cc_final: 0.8534 (m-80) REVERT: A 272 GLU cc_start: 0.8587 (tp30) cc_final: 0.8049 (tp30) REVERT: A 325 MET cc_start: 0.7927 (ptp) cc_final: 0.6904 (ppp) REVERT: A 368 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7421 (tp30) REVERT: A 582 ASP cc_start: 0.8848 (t0) cc_final: 0.8592 (t0) REVERT: A 653 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7069 (p90) REVERT: B 27 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8193 (mp0) REVERT: B 32 MET cc_start: 0.7737 (pmm) cc_final: 0.7277 (pmm) REVERT: B 76 ASP cc_start: 0.7999 (p0) cc_final: 0.7744 (p0) REVERT: B 121 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6262 (m170) REVERT: B 127 GLU cc_start: 0.8420 (tp30) cc_final: 0.8201 (tp30) REVERT: B 221 MET cc_start: 0.8631 (mtp) cc_final: 0.8405 (mtt) REVERT: B 249 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.7070 (p) REVERT: B 261 LEU cc_start: 0.8519 (mp) cc_final: 0.8284 (tp) REVERT: B 278 MET cc_start: 0.6592 (mmt) cc_final: 0.5952 (tpp) REVERT: B 298 LEU cc_start: 0.7745 (pp) cc_final: 0.7543 (pp) REVERT: C 43 GLU cc_start: 0.9026 (pt0) cc_final: 0.8511 (pm20) REVERT: C 57 ILE cc_start: 0.8835 (mm) cc_final: 0.8576 (mt) REVERT: C 127 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6505 (mppt) REVERT: C 148 TRP cc_start: 0.6639 (m100) cc_final: 0.6144 (m100) REVERT: C 157 TYR cc_start: 0.2693 (m-80) cc_final: 0.1796 (m-80) REVERT: D 84 ASP cc_start: 0.8746 (t0) cc_final: 0.8051 (t70) REVERT: D 109 MET cc_start: 0.7205 (mmt) cc_final: 0.6740 (mtt) REVERT: D 199 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7374 (tm-30) REVERT: E 37 TYR cc_start: 0.8621 (t80) cc_final: 0.8374 (t80) outliers start: 69 outliers final: 61 residues processed: 208 average time/residue: 0.2123 time to fit residues: 69.0400 Evaluate side-chains 209 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 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 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 121 HIS Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 43 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 192 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 104 ILE 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 143 optimal weight: 0.7980 chunk 151 optimal weight: 0.2980 chunk 138 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 0.0670 chunk 45 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13255 Z= 0.164 Angle : 0.644 8.844 18006 Z= 0.331 Chirality : 0.045 0.202 1978 Planarity : 0.004 0.033 2374 Dihedral : 5.532 52.630 1832 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.49 % Allowed : 23.14 % Favored : 73.36 % 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: -3.09 (0.20), residues: 1643 helix: 0.48 (0.27), residues: 355 sheet: -2.85 (0.23), residues: 411 loop : -2.80 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 191 HIS 0.005 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.034 0.002 TYR C 197 ARG 0.008 0.000 ARG D 223 *********************** 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 218 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8969 (mm-30) REVERT: A 142 TYR cc_start: 0.8735 (m-10) cc_final: 0.8242 (m-80) REVERT: A 147 TYR cc_start: 0.8843 (m-80) cc_final: 0.8596 (m-80) REVERT: A 191 ASP cc_start: 0.9135 (p0) cc_final: 0.7882 (t0) REVERT: A 192 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8133 (pp20) REVERT: A 272 GLU cc_start: 0.8495 (tp30) cc_final: 0.8274 (tp30) REVERT: A 325 MET cc_start: 0.7875 (ptp) cc_final: 0.6854 (ppp) REVERT: A 368 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 582 ASP cc_start: 0.8863 (t0) cc_final: 0.8600 (t0) REVERT: A 663 PHE cc_start: 0.7896 (m-80) cc_final: 0.7696 (m-10) REVERT: A 801 GLN cc_start: 0.7788 (mt0) cc_final: 0.7530 (mp10) REVERT: B 27 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8293 (mp0) REVERT: B 32 MET cc_start: 0.7562 (pmm) cc_final: 0.7129 (pmm) REVERT: B 76 ASP cc_start: 0.7891 (p0) cc_final: 0.7509 (p0) REVERT: B 221 MET cc_start: 0.8565 (mtp) cc_final: 0.8364 (mtt) REVERT: B 249 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6638 (p) REVERT: B 261 LEU cc_start: 0.8637 (mp) cc_final: 0.8357 (tp) REVERT: B 278 MET cc_start: 0.6630 (mmt) cc_final: 0.6092 (tpp) REVERT: C 43 GLU cc_start: 0.8880 (pt0) cc_final: 0.8488 (pm20) REVERT: C 57 ILE cc_start: 0.8700 (mm) cc_final: 0.8416 (mt) REVERT: C 148 TRP cc_start: 0.6932 (m100) cc_final: 0.6446 (m100) REVERT: C 157 TYR cc_start: 0.1543 (m-80) cc_final: 0.1068 (m-80) REVERT: C 194 MET cc_start: 0.4845 (tmm) cc_final: 0.4555 (tmm) REVERT: D 84 ASP cc_start: 0.8592 (t0) cc_final: 0.7880 (t70) REVERT: D 109 MET cc_start: 0.7218 (mmt) cc_final: 0.6960 (mtt) REVERT: D 111 MET cc_start: 0.8114 (tpp) cc_final: 0.7306 (mpp) REVERT: E 36 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8029 (t0) REVERT: E 37 TYR cc_start: 0.8785 (t80) cc_final: 0.8463 (t80) REVERT: E 96 ASN cc_start: 0.8542 (t0) cc_final: 0.8154 (t0) outliers start: 46 outliers final: 39 residues processed: 213 average time/residue: 0.2094 time to fit residues: 68.8899 Evaluate side-chains 197 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS 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 72 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 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 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 ASN 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 96 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 0.0770 chunk 108 optimal weight: 9.9990 chunk 163 optimal weight: 0.4980 chunk 150 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13255 Z= 0.165 Angle : 0.651 8.972 18006 Z= 0.334 Chirality : 0.045 0.203 1978 Planarity : 0.004 0.040 2374 Dihedral : 5.367 52.161 1832 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 3.42 % Allowed : 24.02 % 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: -2.93 (0.20), residues: 1643 helix: 0.61 (0.28), residues: 356 sheet: -2.63 (0.23), residues: 408 loop : -2.77 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.029 0.001 TYR E 37 ARG 0.005 0.000 ARG C 83 ********************** 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 209 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.9160 (ptp) cc_final: 0.8616 (mtm) REVERT: A 120 ARG cc_start: 0.7253 (ptp90) cc_final: 0.6657 (ptp90) REVERT: A 142 TYR cc_start: 0.8725 (m-10) cc_final: 0.8240 (m-80) REVERT: A 147 TYR cc_start: 0.8819 (m-80) cc_final: 0.8557 (m-80) REVERT: A 191 ASP cc_start: 0.9138 (p0) cc_final: 0.7963 (t0) REVERT: A 192 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8202 (pp20) REVERT: A 272 GLU cc_start: 0.8535 (tp30) cc_final: 0.8282 (tp30) REVERT: A 325 MET cc_start: 0.7895 (ptp) cc_final: 0.6874 (ppp) REVERT: A 368 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 554 GLU cc_start: 0.7747 (mm-30) cc_final: 0.6765 (mp0) REVERT: A 582 ASP cc_start: 0.8866 (t0) cc_final: 0.8605 (t0) REVERT: A 663 PHE cc_start: 0.7857 (m-80) cc_final: 0.7645 (m-10) REVERT: A 801 GLN cc_start: 0.7767 (mt0) cc_final: 0.7507 (mp10) REVERT: B 121 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.5724 (m170) REVERT: B 221 MET cc_start: 0.8610 (mtp) cc_final: 0.8400 (mtt) REVERT: B 249 THR cc_start: 0.6213 (OUTLIER) cc_final: 0.5648 (p) REVERT: B 261 LEU cc_start: 0.8567 (mp) cc_final: 0.8366 (tp) REVERT: B 278 MET cc_start: 0.6668 (mmt) cc_final: 0.6094 (tpp) REVERT: C 41 TYR cc_start: 0.7643 (p90) cc_final: 0.7442 (p90) REVERT: C 43 GLU cc_start: 0.8869 (pt0) cc_final: 0.8422 (pm20) REVERT: C 57 ILE cc_start: 0.8696 (mm) cc_final: 0.8399 (mt) REVERT: C 148 TRP cc_start: 0.6909 (m100) cc_final: 0.6484 (m100) REVERT: C 157 TYR cc_start: 0.1585 (m-80) cc_final: 0.1103 (m-80) REVERT: D 84 ASP cc_start: 0.8563 (t0) cc_final: 0.7833 (t70) REVERT: D 109 MET cc_start: 0.7213 (mmt) cc_final: 0.6831 (mtt) REVERT: D 111 MET cc_start: 0.8192 (tpp) cc_final: 0.7408 (mpp) REVERT: E 36 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7730 (t0) REVERT: E 37 TYR cc_start: 0.8666 (t80) cc_final: 0.8423 (t80) REVERT: E 96 ASN cc_start: 0.8591 (t0) cc_final: 0.8214 (t0) outliers start: 45 outliers final: 40 residues processed: 204 average time/residue: 0.2055 time to fit residues: 66.0119 Evaluate side-chains 197 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE 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 532 VAL Chi-restraints excluded: chain A residue 555 HIS 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 121 HIS Chi-restraints excluded: chain B residue 156 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 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 ASN 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 103 optimal weight: 0.0060 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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** E 36 ASN ** E 103 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 = 0.3853 r_free = 0.3853 target = 0.121760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094143 restraints weight = 70588.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096997 restraints weight = 24983.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099273 restraints weight = 14068.461| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13255 Z= 0.177 Angle : 0.646 10.396 18006 Z= 0.333 Chirality : 0.044 0.210 1978 Planarity : 0.004 0.040 2374 Dihedral : 5.331 51.901 1832 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.57 % Allowed : 24.31 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.20), residues: 1643 helix: 0.71 (0.28), residues: 356 sheet: -2.52 (0.24), residues: 413 loop : -2.73 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.001 PHE A 478 TYR 0.023 0.001 TYR C 41 ARG 0.006 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.38 seconds wall clock time: 49 minutes 2.85 seconds (2942.85 seconds total)