Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:22:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/04_2023/7tmw_26003_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/04_2023/7tmw_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_26003/04_2023/7tmw_26003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/04_2023/7tmw_26003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/04_2023/7tmw_26003_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmw_26003/04_2023/7tmw_26003_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.38, per 1000 atoms: 0.60 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: 2.93 Conformation dependent library (CDL) restraints added in 1.1 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: 0.45 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: 2.59 Time building geometry restraints manager: 3.16 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: 0.970 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: 5.340 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.854 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2603 time to fit residues: 53.1960 Evaluate side-chains 147 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2293 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7481 Z= 0.225 Angle : 0.570 8.070 10139 Z= 0.302 Chirality : 0.043 0.168 1147 Planarity : 0.005 0.070 1277 Dihedral : 4.497 21.107 1003 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.14 % 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: 1.54 (0.29), residues: 339 sheet: -0.66 (0.35), residues: 207 loop : -1.11 (0.31), residues: 360 *********************** 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 161 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 154 average time/residue: 0.2612 time to fit residues: 50.7830 Evaluate side-chains 156 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0696 time to fit residues: 2.0983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 7481 Z= 0.204 Angle : 0.539 7.423 10139 Z= 0.287 Chirality : 0.043 0.151 1147 Planarity : 0.004 0.054 1277 Dihedral : 4.398 16.444 1003 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.41 % 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: 0.13 (0.28), residues: 906 helix: 1.76 (0.29), residues: 337 sheet: -0.62 (0.35), residues: 208 loop : -1.05 (0.32), residues: 361 *********************** 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 172 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 163 average time/residue: 0.2208 time to fit residues: 47.1191 Evaluate side-chains 159 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0734 time to fit residues: 2.1398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 82 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7481 Z= 0.194 Angle : 0.520 7.321 10139 Z= 0.278 Chirality : 0.042 0.142 1147 Planarity : 0.004 0.046 1277 Dihedral : 4.347 16.959 1003 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 1.78 % 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: 1.74 (0.29), residues: 344 sheet: -0.50 (0.35), residues: 208 loop : -1.05 (0.32), residues: 354 *********************** 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 158 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 149 average time/residue: 0.2663 time to fit residues: 50.1667 Evaluate side-chains 151 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0712 time to fit residues: 2.1952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 78 optimal weight: 0.0070 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 608 GLN R 673 ASN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 7481 Z= 0.187 Angle : 0.512 7.058 10139 Z= 0.274 Chirality : 0.042 0.133 1147 Planarity : 0.004 0.044 1277 Dihedral : 4.289 18.169 1003 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 2.41 % 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 (0.29), residues: 906 helix: 2.02 (0.29), residues: 337 sheet: -0.41 (0.35), residues: 215 loop : -1.06 (0.33), residues: 354 *********************** 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 166 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 158 average time/residue: 0.2628 time to fit residues: 52.6729 Evaluate side-chains 148 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0755 time to fit residues: 2.2745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 ** R1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 7481 Z= 0.259 Angle : 0.584 11.284 10139 Z= 0.307 Chirality : 0.044 0.274 1147 Planarity : 0.004 0.042 1277 Dihedral : 4.484 17.383 1003 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.28 % 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: 1.63 (0.28), residues: 344 sheet: -0.39 (0.36), residues: 217 loop : -1.12 (0.33), residues: 345 *********************** 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 165 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 155 average time/residue: 0.2740 time to fit residues: 53.2717 Evaluate side-chains 158 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0778 time to fit residues: 2.4272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 473 ASN ** 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: 0.6437 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 7481 Z= 0.283 Angle : 0.596 11.350 10139 Z= 0.315 Chirality : 0.045 0.279 1147 Planarity : 0.004 0.041 1277 Dihedral : 4.664 21.010 1003 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 2.66 % 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: 0.06 (0.28), residues: 906 helix: 1.65 (0.28), residues: 337 sheet: -0.49 (0.37), residues: 207 loop : -1.16 (0.31), residues: 362 *********************** 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 178 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 170 average time/residue: 0.2517 time to fit residues: 54.5925 Evaluate side-chains 156 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1125 time to fit residues: 2.5575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.0570 chunk 59 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 78 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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 608 GLN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 7481 Z= 0.157 Angle : 0.547 10.143 10139 Z= 0.291 Chirality : 0.044 0.263 1147 Planarity : 0.004 0.039 1277 Dihedral : 4.358 20.286 1003 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.40 % 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: 0.42 (0.29), residues: 906 helix: 2.04 (0.29), residues: 337 sheet: -0.37 (0.35), residues: 217 loop : -1.01 (0.32), residues: 352 *********************** 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 166 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 159 average time/residue: 0.2568 time to fit residues: 52.0984 Evaluate side-chains 156 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0912 time to fit residues: 2.1694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.6451 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 7481 Z= 0.320 Angle : 0.642 11.322 10139 Z= 0.339 Chirality : 0.047 0.277 1147 Planarity : 0.004 0.039 1277 Dihedral : 4.735 22.438 1003 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 1.27 % 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: 0.11 (0.28), residues: 906 helix: 1.65 (0.28), residues: 337 sheet: -0.59 (0.37), residues: 202 loop : -0.99 (0.31), residues: 367 *********************** 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 167 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 161 average time/residue: 0.2558 time to fit residues: 52.2618 Evaluate side-chains 160 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0802 time to fit residues: 2.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 89 optimal weight: 0.5980 chunk 82 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.0030 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.2086 ------------------------------------------------------------------------------- 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 608 GLN ** R1215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 7481 Z= 0.178 Angle : 0.576 9.995 10139 Z= 0.305 Chirality : 0.044 0.277 1147 Planarity : 0.004 0.043 1277 Dihedral : 4.465 20.936 1003 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.89 % 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: 0.31 (0.28), residues: 906 helix: 1.91 (0.28), residues: 337 sheet: -0.47 (0.35), residues: 217 loop : -1.00 (0.32), residues: 352 ********************** 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 164 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 160 average time/residue: 0.2563 time to fit residues: 52.0217 Evaluate side-chains 156 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0873 time to fit residues: 1.6890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** R1222 GLN ** R1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 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 = 0.4290 r_free = 0.4290 target = 0.163282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.148785 restraints weight = 11152.251| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.46 r_work: 0.4015 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3044 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= 0.230 Angle : 0.610 10.278 10139 Z= 0.321 Chirality : 0.045 0.279 1147 Planarity : 0.004 0.051 1277 Dihedral : 4.554 20.922 1003 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.76 % 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: 0.29 (0.28), residues: 906 helix: 1.84 (0.28), residues: 337 sheet: -0.43 (0.35), residues: 216 loop : -1.00 (0.32), residues: 353 =============================================================================== Job complete usr+sys time: 2083.68 seconds wall clock time: 38 minutes 7.11 seconds (2287.11 seconds total)