Starting phenix.real_space_refine on Tue Feb 13 19:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/02_2024/7tmw_26003_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/02_2024/7tmw_26003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/02_2024/7tmw_26003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/02_2024/7tmw_26003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/02_2024/7tmw_26003_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/02_2024/7tmw_26003_neut.pdb" } resolution = 3.2 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= 0.001 sd= 0.936 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 49 5.16 5 C 4695 2.51 5 N 1242 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 1011": "OE1" <-> "OE2" Residue "R GLU 1204": "OE1" <-> "OE2" Residue "R GLU 1329": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7320 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4075 Classifications: {'peptide': 499} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2273 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 2, 'TRANS': 4} Chain: "N" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.50, per 1000 atoms: 0.61 Number of scatterers: 7320 At special positions: 0 Unit cell: (124.02, 95.4, 92.22, 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 49 16.00 O 1334 8.00 N 1242 7.00 C 4695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 485 " - pdb=" SG CYS R 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 39.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'R' and resid 405 through 430 Processing helix chain 'R' and resid 437 through 468 Processing helix chain 'R' and resid 475 through 482 Processing helix chain 'R' and resid 482 through 515 removed outlier: 4.131A pdb=" N GLN R 486 " --> pdb=" O SER R 482 " (cutoff:3.500A) Processing helix chain 'R' and resid 524 through 549 Proline residue: R 546 - end of helix Processing helix chain 'R' and resid 549 through 554 Processing helix chain 'R' and resid 573 through 584 removed outlier: 4.622A pdb=" N TYR R 579 " --> pdb=" O GLY R 575 " (cutoff:3.500A) Processing helix chain 'R' and resid 587 through 608 Processing helix chain 'R' and resid 624 through 653 Proline residue: R 643 - end of helix Processing helix chain 'R' and resid 658 through 668 removed outlier: 3.836A pdb=" N THR R 662 " --> pdb=" O PRO R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 681 Proline residue: R 678 - end of helix Processing helix chain 'R' and resid 685 through 699 removed outlier: 3.514A pdb=" N LYS R 689 " --> pdb=" O THR R 685 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1034 Processing helix chain 'R' and resid 1047 through 1058 removed outlier: 3.636A pdb=" N ILE R1051 " --> pdb=" O GLY R1047 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL R1052 " --> pdb=" O LYS R1048 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R1057 " --> pdb=" O LYS R1053 " (cutoff:3.500A) Processing helix chain 'R' and resid 1229 through 1233 removed outlier: 3.601A pdb=" N CYS R1232 " --> pdb=" O TRP R1229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R1233 " --> pdb=" O ILE R1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1229 through 1233' Processing helix chain 'R' and resid 1247 through 1264 Processing helix chain 'R' and resid 1278 through 1289 Processing helix chain 'R' and resid 1292 through 1297 removed outlier: 3.849A pdb=" N TYR R1296 " --> pdb=" O LYS R1292 " (cutoff:3.500A) Processing helix chain 'R' and resid 1298 through 1303 removed outlier: 3.771A pdb=" N TYR R1303 " --> pdb=" O PHE R1300 " (cutoff:3.500A) Processing helix chain 'R' and resid 1316 through 1336 removed outlier: 3.544A pdb=" N THR R1320 " --> pdb=" O ASP R1316 " (cutoff:3.500A) Processing helix chain 'R' and resid 1355 through 1376 Processing helix chain 'N' and resid 61 through 66 removed outlier: 4.515A pdb=" N GLY N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 1206 through 1209 removed outlier: 6.476A pdb=" N HIS R1036 " --> pdb=" O HIS R1215 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE R1217 " --> pdb=" O HIS R1036 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU R1038 " --> pdb=" O PHE R1217 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ALA R1238 " --> pdb=" O THR R1035 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG R1037 " --> pdb=" O ALA R1238 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE R1240 " --> pdb=" O ARG R1037 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU R1039 " --> pdb=" O ILE R1240 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL R1242 " --> pdb=" O LEU R1039 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU R1041 " --> pdb=" O VAL R1242 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP R1244 " --> pdb=" O LEU R1041 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE R1239 " --> pdb=" O ILE R1273 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE R1275 " --> pdb=" O ILE R1239 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE R1241 " --> pdb=" O PHE R1275 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN R1277 " --> pdb=" O PHE R1241 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL R1243 " --> pdb=" O ASN R1277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL R1272 " --> pdb=" O TYR R1345 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS R1347 " --> pdb=" O VAL R1272 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU R1274 " --> pdb=" O HIS R1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61 removed outlier: 3.719A pdb=" N ARG B 59 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 72 removed outlier: 7.010A pdb=" N ALA B 83 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 71 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 81 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B 101 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 93 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS B 99 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 115 removed outlier: 5.687A pdb=" N ASN B 135 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 145 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.660A pdb=" N CYS B 158 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 180 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 186 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 288 removed outlier: 3.981A pdb=" N SER B 285 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP B 308 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG B 314 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.700A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.611A pdb=" N GLU N 46 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 2.96 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: 2341 1.34 - 1.46: 1885 1.46 - 1.59: 3188 1.59 - 1.71: 0 1.71 - 1.83: 67 Bond restraints: 7481 Sorted by residual: bond pdb=" CG GLU R1329 " pdb=" CD GLU R1329 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.43e+00 bond pdb=" C ILE R 642 " pdb=" N PRO R 643 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.23e-02 6.61e+03 1.18e+00 bond pdb=" CG PRO R 671 " pdb=" CD PRO R 671 " ideal model delta sigma weight residual 1.503 1.469 0.034 3.40e-02 8.65e+02 1.00e+00 bond pdb=" CB GLU R1329 " pdb=" CG GLU R1329 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" N GLU R1329 " pdb=" CA GLU R1329 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.28e-02 6.10e+03 8.79e-01 ... (remaining 7476 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.07: 93 105.07 - 112.39: 3769 112.39 - 119.70: 2556 119.70 - 127.02: 3640 127.02 - 134.33: 81 Bond angle restraints: 10139 Sorted by residual: angle pdb=" N GLU R1329 " pdb=" CA GLU R1329 " pdb=" CB GLU R1329 " ideal model delta sigma weight residual 110.28 116.39 -6.11 1.55e+00 4.16e-01 1.56e+01 angle pdb=" CB ARG R1327 " pdb=" CG ARG R1327 " pdb=" CD ARG R1327 " ideal model delta sigma weight residual 111.30 119.93 -8.63 2.30e+00 1.89e-01 1.41e+01 angle pdb=" N VAL B 100 " pdb=" CA VAL B 100 " pdb=" C VAL B 100 " ideal model delta sigma weight residual 113.53 110.20 3.33 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA PRO R 546 " pdb=" N PRO R 546 " pdb=" CD PRO R 546 " ideal model delta sigma weight residual 112.00 107.34 4.66 1.40e+00 5.10e-01 1.11e+01 angle pdb=" CG ARG B 324 " pdb=" CD ARG B 324 " pdb=" NE ARG B 324 " ideal model delta sigma weight residual 112.00 118.76 -6.76 2.20e+00 2.07e-01 9.44e+00 ... (remaining 10134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3968 17.20 - 34.40: 359 34.40 - 51.60: 60 51.60 - 68.79: 5 68.79 - 85.99: 6 Dihedral angle restraints: 4398 sinusoidal: 1705 harmonic: 2693 Sorted by residual: dihedral pdb=" CB CYS R 485 " pdb=" SG CYS R 485 " pdb=" SG CYS R 563 " pdb=" CB CYS R 563 " ideal model delta sinusoidal sigma weight residual -86.00 -120.04 34.04 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA MET R1055 " pdb=" C MET R1055 " pdb=" N ARG R1056 " pdb=" CA ARG R1056 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TRP B 92 " pdb=" C TRP B 92 " pdb=" N ASP B 93 " pdb=" CA ASP B 93 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 808 0.044 - 0.087: 237 0.087 - 0.131: 89 0.131 - 0.175: 9 0.175 - 0.219: 4 Chirality restraints: 1147 Sorted by residual: chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL N 37 " pdb=" CA VAL N 37 " pdb=" CG1 VAL N 37 " pdb=" CG2 VAL N 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CG LEU B 346 " pdb=" CB LEU B 346 " pdb=" CD1 LEU B 346 " pdb=" CD2 LEU B 346 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 1144 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 664 " -0.026 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP R 664 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP R 664 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 664 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 664 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 664 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 664 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 545 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO R 546 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 546 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 546 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 109 " 0.023 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP B 109 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 109 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 109 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 109 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 109 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 109 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 109 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 109 " -0.001 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 450 2.73 - 3.28: 7442 3.28 - 3.82: 12428 3.82 - 4.36: 14502 4.36 - 4.90: 25054 Nonbonded interactions: 59876 Sorted by model distance: nonbonded pdb=" OG SER B 84 " pdb=" OD1 ASP B 86 " model vdw 2.193 2.440 nonbonded pdb=" O VAL R 542 " pdb=" OH TYR R 579 " model vdw 2.250 2.440 nonbonded pdb=" OG SER B 237 " pdb=" O PRO N 100 " model vdw 2.255 2.440 nonbonded pdb=" O ALA R 543 " pdb=" OH TYR R 557 " model vdw 2.262 2.440 nonbonded pdb=" O ILE B 133 " pdb=" OG SER B 146 " model vdw 2.266 2.440 ... (remaining 59871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 5.090 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.300 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 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 : 0.003 0.046 7481 Z= 0.219 Angle : 0.701 10.213 10139 Z= 0.382 Chirality : 0.048 0.219 1147 Planarity : 0.006 0.111 1277 Dihedral : 13.225 85.993 2646 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 906 helix: 1.33 (0.29), residues: 326 sheet: -0.69 (0.34), residues: 210 loop : -1.22 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP R 664 HIS 0.003 0.001 HIS R1342 PHE 0.037 0.002 PHE R1325 TYR 0.016 0.002 TYR N 32 ARG 0.009 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: R 447 LEU cc_start: 0.7776 (tp) cc_final: 0.7549 (tp) REVERT: R 467 LYS cc_start: 0.7077 (tptm) cc_final: 0.6724 (mttt) REVERT: R 1019 LYS cc_start: 0.7276 (mtpp) cc_final: 0.7022 (mtpp) REVERT: R 1299 GLU cc_start: 0.7579 (mp0) cc_final: 0.7346 (mp0) REVERT: B 323 ASN cc_start: 0.7941 (m-40) cc_final: 0.7732 (m-40) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2527 time to fit residues: 51.7271 Evaluate side-chains 149 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1249 ASN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7481 Z= 0.219 Angle : 0.565 8.042 10139 Z= 0.300 Chirality : 0.043 0.168 1147 Planarity : 0.005 0.073 1277 Dihedral : 4.486 21.455 1003 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.14 % Allowed : 10.41 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.28), residues: 906 helix: 1.55 (0.29), residues: 339 sheet: -0.66 (0.35), residues: 207 loop : -1.11 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 664 HIS 0.003 0.001 HIS R1347 PHE 0.020 0.002 PHE B 209 TYR 0.012 0.002 TYR N 94 ARG 0.008 0.000 ARG R1327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1019 LYS cc_start: 0.7306 (mtpp) cc_final: 0.7056 (mtpp) REVERT: R 1228 LYS cc_start: 0.7050 (mptt) cc_final: 0.6843 (mmtm) REVERT: R 1242 VAL cc_start: 0.7645 (p) cc_final: 0.7425 (t) REVERT: B 242 ILE cc_start: 0.8084 (tt) cc_final: 0.7441 (tp) REVERT: B 305 ASN cc_start: 0.6955 (m-40) cc_final: 0.6687 (t0) REVERT: B 323 ASN cc_start: 0.7960 (m-40) cc_final: 0.7642 (m-40) outliers start: 9 outliers final: 7 residues processed: 153 average time/residue: 0.2537 time to fit residues: 48.8301 Evaluate side-chains 152 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 chunk 22 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 0.3072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 608 GLN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7481 Z= 0.171 Angle : 0.520 7.119 10139 Z= 0.278 Chirality : 0.042 0.140 1147 Planarity : 0.004 0.053 1277 Dihedral : 4.297 16.248 1003 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 12.31 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 906 helix: 1.65 (0.29), residues: 344 sheet: -0.59 (0.35), residues: 208 loop : -0.99 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 664 HIS 0.003 0.001 HIS R1342 PHE 0.024 0.001 PHE R 459 TYR 0.017 0.001 TYR R1032 ARG 0.007 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 449 CYS cc_start: 0.5167 (m) cc_final: 0.4737 (m) REVERT: R 595 ILE cc_start: 0.5048 (OUTLIER) cc_final: 0.4629 (mm) REVERT: R 599 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: R 1019 LYS cc_start: 0.7272 (mtpp) cc_final: 0.7022 (mtpp) REVERT: R 1299 GLU cc_start: 0.7642 (mp0) cc_final: 0.7420 (mp0) REVERT: B 242 ILE cc_start: 0.8071 (tt) cc_final: 0.7429 (tp) REVERT: B 305 ASN cc_start: 0.6997 (m-40) cc_final: 0.6643 (t0) REVERT: B 323 ASN cc_start: 0.7876 (m-40) cc_final: 0.7525 (m-40) outliers start: 19 outliers final: 9 residues processed: 158 average time/residue: 0.2316 time to fit residues: 46.8325 Evaluate side-chains 158 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.0040 chunk 82 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7481 Z= 0.187 Angle : 0.518 7.147 10139 Z= 0.276 Chirality : 0.042 0.134 1147 Planarity : 0.004 0.046 1277 Dihedral : 4.248 16.047 1003 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.92 % Allowed : 14.09 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 906 helix: 1.74 (0.29), residues: 344 sheet: -0.47 (0.36), residues: 208 loop : -0.99 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 664 HIS 0.003 0.001 HIS R1342 PHE 0.020 0.001 PHE R 597 TYR 0.018 0.001 TYR R1032 ARG 0.006 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 449 CYS cc_start: 0.5145 (m) cc_final: 0.4732 (m) REVERT: R 483 THR cc_start: 0.7482 (p) cc_final: 0.7226 (m) REVERT: R 595 ILE cc_start: 0.5153 (OUTLIER) cc_final: 0.4716 (mm) REVERT: R 599 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: R 1011 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7178 (mp0) REVERT: R 1019 LYS cc_start: 0.7283 (mtpp) cc_final: 0.7043 (mtpp) REVERT: R 1299 GLU cc_start: 0.7670 (mp0) cc_final: 0.7365 (mp0) REVERT: B 272 MET cc_start: 0.6080 (tpp) cc_final: 0.5744 (tpp) REVERT: B 305 ASN cc_start: 0.7014 (m-40) cc_final: 0.6660 (t0) REVERT: B 323 ASN cc_start: 0.7836 (m-40) cc_final: 0.7485 (m-40) outliers start: 23 outliers final: 14 residues processed: 162 average time/residue: 0.2327 time to fit residues: 48.7517 Evaluate side-chains 166 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 44 optimal weight: 0.0070 chunk 78 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 423 ASN R 608 GLN R 677 ASN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7481 Z= 0.232 Angle : 0.541 7.490 10139 Z= 0.290 Chirality : 0.042 0.149 1147 Planarity : 0.004 0.044 1277 Dihedral : 4.366 16.823 1003 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.19 % Allowed : 14.97 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 906 helix: 1.68 (0.28), residues: 344 sheet: -0.41 (0.36), residues: 214 loop : -0.98 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R1229 HIS 0.003 0.001 HIS R1215 PHE 0.021 0.002 PHE R1325 TYR 0.019 0.001 TYR R1032 ARG 0.006 0.001 ARG R1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 449 CYS cc_start: 0.5005 (m) cc_final: 0.4583 (m) REVERT: R 595 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.4865 (mm) REVERT: R 599 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: R 1019 LYS cc_start: 0.7284 (mtpp) cc_final: 0.7037 (mtpp) REVERT: R 1218 ASP cc_start: 0.7120 (p0) cc_final: 0.6491 (p0) REVERT: R 1299 GLU cc_start: 0.7679 (mp0) cc_final: 0.7399 (mp0) REVERT: B 242 ILE cc_start: 0.8072 (tt) cc_final: 0.7532 (tp) REVERT: B 272 MET cc_start: 0.6167 (tpp) cc_final: 0.5928 (tpp) REVERT: B 305 ASN cc_start: 0.7032 (m-40) cc_final: 0.6626 (t0) REVERT: B 323 ASN cc_start: 0.7756 (m-40) cc_final: 0.7397 (m-40) outliers start: 33 outliers final: 19 residues processed: 166 average time/residue: 0.2523 time to fit residues: 53.0007 Evaluate side-chains 167 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 525 LYS Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 608 GLN Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 608 GLN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7481 Z= 0.309 Angle : 0.611 11.815 10139 Z= 0.323 Chirality : 0.045 0.280 1147 Planarity : 0.004 0.040 1277 Dihedral : 4.607 17.463 1003 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.57 % Allowed : 15.23 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 906 helix: 1.43 (0.28), residues: 346 sheet: -0.42 (0.36), residues: 216 loop : -1.07 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 221 HIS 0.004 0.001 HIS R1347 PHE 0.022 0.002 PHE R 597 TYR 0.021 0.002 TYR R1032 ARG 0.006 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 449 CYS cc_start: 0.5353 (m) cc_final: 0.4958 (m) REVERT: R 599 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: R 1019 LYS cc_start: 0.7182 (mtpp) cc_final: 0.6943 (mtpp) REVERT: R 1218 ASP cc_start: 0.7173 (p0) cc_final: 0.6476 (p0) REVERT: R 1285 LYS cc_start: 0.5396 (ttmt) cc_final: 0.4738 (tttt) REVERT: R 1299 GLU cc_start: 0.7670 (mp0) cc_final: 0.7321 (mp0) REVERT: B 109 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.6603 (p-90) REVERT: B 242 ILE cc_start: 0.8058 (tt) cc_final: 0.7604 (tp) REVERT: B 305 ASN cc_start: 0.7046 (m-40) cc_final: 0.6732 (m-40) REVERT: B 323 ASN cc_start: 0.7808 (m-40) cc_final: 0.7448 (m-40) outliers start: 36 outliers final: 24 residues processed: 172 average time/residue: 0.2559 time to fit residues: 55.2923 Evaluate side-chains 176 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 510 LYS Chi-restraints excluded: chain R residue 525 LYS Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 608 GLN Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1216 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7481 Z= 0.217 Angle : 0.574 11.340 10139 Z= 0.302 Chirality : 0.043 0.247 1147 Planarity : 0.004 0.039 1277 Dihedral : 4.452 19.377 1003 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.19 % Allowed : 17.26 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.28), residues: 906 helix: 1.71 (0.28), residues: 337 sheet: -0.42 (0.36), residues: 216 loop : -1.10 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R1229 HIS 0.003 0.001 HIS R1342 PHE 0.032 0.002 PHE R 411 TYR 0.025 0.001 TYR R1032 ARG 0.005 0.000 ARG R1037 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 449 CYS cc_start: 0.5330 (m) cc_final: 0.4936 (m) REVERT: R 467 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6513 (mtmm) REVERT: R 595 ILE cc_start: 0.5143 (OUTLIER) cc_final: 0.4848 (mm) REVERT: R 599 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: R 1019 LYS cc_start: 0.7335 (mtpp) cc_final: 0.7090 (mtpp) REVERT: R 1044 ASP cc_start: 0.7244 (m-30) cc_final: 0.7023 (m-30) REVERT: R 1055 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6500 (mpm) REVERT: R 1218 ASP cc_start: 0.7131 (p0) cc_final: 0.6478 (p0) REVERT: R 1285 LYS cc_start: 0.5277 (ttmt) cc_final: 0.4576 (tttt) REVERT: R 1299 GLU cc_start: 0.7617 (mp0) cc_final: 0.7321 (mp0) REVERT: B 62 ARG cc_start: 0.6540 (mtt-85) cc_final: 0.5902 (mtt-85) REVERT: B 109 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6536 (p-90) REVERT: B 305 ASN cc_start: 0.7009 (m-40) cc_final: 0.6718 (m-40) REVERT: B 323 ASN cc_start: 0.7804 (m-40) cc_final: 0.7454 (m-40) REVERT: B 345 PHE cc_start: 0.7599 (m-10) cc_final: 0.6538 (m-10) outliers start: 33 outliers final: 18 residues processed: 168 average time/residue: 0.2578 time to fit residues: 54.7774 Evaluate side-chains 169 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 525 LYS Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.0050 chunk 83 optimal weight: 0.0870 chunk 75 optimal weight: 0.8980 overall best weight: 0.1972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7481 Z= 0.164 Angle : 0.543 9.467 10139 Z= 0.290 Chirality : 0.043 0.269 1147 Planarity : 0.003 0.038 1277 Dihedral : 4.274 20.471 1003 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.92 % Allowed : 18.65 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 906 helix: 1.98 (0.29), residues: 337 sheet: -0.42 (0.36), residues: 217 loop : -1.02 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 664 HIS 0.003 0.001 HIS R1342 PHE 0.050 0.002 PHE R 411 TYR 0.025 0.001 TYR R1032 ARG 0.005 0.000 ARG R1037 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 412 VAL cc_start: 0.6638 (OUTLIER) cc_final: 0.5924 (m) REVERT: R 449 CYS cc_start: 0.5297 (m) cc_final: 0.4900 (m) REVERT: R 599 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: R 1019 LYS cc_start: 0.7229 (mtpp) cc_final: 0.6984 (mtpp) REVERT: R 1044 ASP cc_start: 0.7184 (m-30) cc_final: 0.6952 (m-30) REVERT: R 1055 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6531 (mpm) REVERT: R 1218 ASP cc_start: 0.7043 (p0) cc_final: 0.6407 (p0) REVERT: R 1285 LYS cc_start: 0.5201 (ttmt) cc_final: 0.4637 (ttmt) REVERT: R 1299 GLU cc_start: 0.7579 (mp0) cc_final: 0.7348 (mp0) REVERT: B 109 TRP cc_start: 0.7571 (OUTLIER) cc_final: 0.6290 (p-90) REVERT: B 305 ASN cc_start: 0.6970 (m-40) cc_final: 0.6684 (m-40) REVERT: B 323 ASN cc_start: 0.7770 (m-40) cc_final: 0.7427 (m-40) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 0.2533 time to fit residues: 52.1246 Evaluate side-chains 166 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7481 Z= 0.287 Angle : 0.610 10.724 10139 Z= 0.324 Chirality : 0.044 0.193 1147 Planarity : 0.004 0.039 1277 Dihedral : 4.611 21.671 1003 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.81 % Allowed : 18.40 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 906 helix: 1.75 (0.28), residues: 337 sheet: -0.40 (0.36), residues: 216 loop : -1.07 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R1229 HIS 0.004 0.001 HIS R1347 PHE 0.027 0.002 PHE R 411 TYR 0.021 0.002 TYR R1032 ARG 0.004 0.001 ARG R1332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 412 VAL cc_start: 0.6822 (OUTLIER) cc_final: 0.5985 (m) REVERT: R 449 CYS cc_start: 0.5411 (m) cc_final: 0.4990 (m) REVERT: R 467 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6560 (mtmm) REVERT: R 595 ILE cc_start: 0.5302 (OUTLIER) cc_final: 0.5018 (mm) REVERT: R 599 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7153 (m-10) REVERT: R 1019 LYS cc_start: 0.7246 (mtpp) cc_final: 0.6985 (mtpp) REVERT: R 1044 ASP cc_start: 0.7192 (m-30) cc_final: 0.6954 (m-30) REVERT: R 1055 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6564 (mpm) REVERT: R 1218 ASP cc_start: 0.7117 (p0) cc_final: 0.6514 (p0) REVERT: R 1285 LYS cc_start: 0.5352 (ttmt) cc_final: 0.4640 (ttmt) REVERT: R 1299 GLU cc_start: 0.7570 (mp0) cc_final: 0.7277 (mp0) REVERT: R 1321 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6858 (ttt-90) REVERT: B 109 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.6483 (p-90) REVERT: B 242 ILE cc_start: 0.8090 (tt) cc_final: 0.7648 (tp) REVERT: B 305 ASN cc_start: 0.6992 (m-40) cc_final: 0.6675 (m-40) REVERT: B 323 ASN cc_start: 0.7790 (m-40) cc_final: 0.7418 (m-40) outliers start: 30 outliers final: 19 residues processed: 168 average time/residue: 0.2458 time to fit residues: 53.7442 Evaluate side-chains 172 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 427 ILE Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 679 ILE Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.0570 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 677 ASN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1375 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7481 Z= 0.250 Angle : 0.599 10.344 10139 Z= 0.319 Chirality : 0.044 0.171 1147 Planarity : 0.004 0.048 1277 Dihedral : 4.613 22.342 1003 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.43 % Allowed : 18.91 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 906 helix: 1.78 (0.28), residues: 337 sheet: -0.43 (0.36), residues: 217 loop : -1.00 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R1229 HIS 0.003 0.001 HIS R1342 PHE 0.038 0.002 PHE R 411 TYR 0.025 0.002 TYR R1032 ARG 0.016 0.001 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 412 VAL cc_start: 0.6726 (OUTLIER) cc_final: 0.6460 (t) REVERT: R 449 CYS cc_start: 0.5342 (m) cc_final: 0.4931 (m) REVERT: R 595 ILE cc_start: 0.5231 (OUTLIER) cc_final: 0.4944 (mm) REVERT: R 599 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: R 1019 LYS cc_start: 0.7306 (mtpp) cc_final: 0.7053 (mtpp) REVERT: R 1044 ASP cc_start: 0.7183 (m-30) cc_final: 0.6941 (m-30) REVERT: R 1055 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6547 (mpm) REVERT: R 1218 ASP cc_start: 0.7101 (p0) cc_final: 0.6511 (p0) REVERT: R 1285 LYS cc_start: 0.5219 (ttmt) cc_final: 0.4498 (ttmt) REVERT: R 1299 GLU cc_start: 0.7524 (mp0) cc_final: 0.7313 (mp0) REVERT: R 1332 ARG cc_start: 0.7445 (ptm-80) cc_final: 0.7002 (ptm-80) REVERT: B 109 TRP cc_start: 0.7754 (OUTLIER) cc_final: 0.6388 (p-90) REVERT: B 223 VAL cc_start: 0.7722 (t) cc_final: 0.7423 (m) REVERT: B 305 ASN cc_start: 0.6995 (m-40) cc_final: 0.6679 (m-40) REVERT: B 323 ASN cc_start: 0.7725 (m-40) cc_final: 0.7372 (m-40) outliers start: 27 outliers final: 22 residues processed: 168 average time/residue: 0.2491 time to fit residues: 53.1651 Evaluate side-chains 179 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 ILE Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 427 ILE Chi-restraints excluded: chain R residue 429 MET Chi-restraints excluded: chain R residue 467 LYS Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 599 TYR Chi-restraints excluded: chain R residue 1052 VAL Chi-restraints excluded: chain R residue 1055 MET Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain R residue 1249 ASN Chi-restraints excluded: chain R residue 1305 THR Chi-restraints excluded: chain R residue 1354 THR Chi-restraints excluded: chain R residue 1356 ASN Chi-restraints excluded: chain R residue 1366 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 109 TRP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 0.0570 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1375 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 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 = 0.4291 r_free = 0.4291 target = 0.163642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.148982 restraints weight = 11183.724| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.46 r_work: 0.4012 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 7481 Z= 0.264 Angle : 0.976 59.199 10139 Z= 0.581 Chirality : 0.050 0.898 1147 Planarity : 0.005 0.085 1277 Dihedral : 4.602 22.404 1003 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.81 % Allowed : 19.04 % Favored : 77.16 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 906 helix: 1.79 (0.28), residues: 337 sheet: -0.44 (0.36), residues: 217 loop : -1.06 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R1229 HIS 0.003 0.001 HIS R1342 PHE 0.030 0.002 PHE R 411 TYR 0.023 0.002 TYR R1032 ARG 0.010 0.000 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.65 seconds wall clock time: 39 minutes 33.90 seconds (2373.90 seconds total)