Starting phenix.real_space_refine on Mon Feb 19 22:04:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/02_2024/8fpj_29366_trim_updated.pdb" } resolution = 2.74 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= 0.002 sd= 0.052 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: 6 Type Number sf(0) Gaussians S 70 5.16 5 C 8157 2.51 5 N 2206 2.21 5 O 2383 1.98 5 F 1 1.80 5 H 13143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 959": "OE1" <-> "OE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1154": "OD1" <-> "OD2" Residue "A GLU 1304": "OE1" <-> "OE2" Residue "A TYR 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "C ASP 209": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25960 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 21983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 21983 Classifications: {'peptide': 1345} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1293} Chain breaks: 2 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1491 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 975 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 736 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "E" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 740 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y6L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.63, per 1000 atoms: 0.49 Number of scatterers: 25960 At special positions: 0 Unit cell: (115.92, 102.48, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 F 1 9.00 O 2383 8.00 N 2206 7.00 C 8157 6.00 H 13143 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 22.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 6 sheets defined 52.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.662A pdb=" N GLN A 82 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS A 83 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 119 removed outlier: 3.867A pdb=" N TRP A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 144 through 166 removed outlier: 3.736A pdb=" N ILE A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 266 through 284 removed outlier: 4.649A pdb=" N GLU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 315 removed outlier: 4.849A pdb=" N LYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 351 through 361 removed outlier: 3.957A pdb=" N TYR A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TYR A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.021A pdb=" N MET A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.566A pdb=" N PHE A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.629A pdb=" N ILE A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 594 No H-bonds generated for 'chain 'A' and resid 591 through 594' Processing helix chain 'A' and resid 645 through 659 removed outlier: 4.443A pdb=" N ILE A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N CYS A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 Proline residue: A 673 - end of helix Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 716 through 733 removed outlier: 3.699A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 728 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 785 removed outlier: 3.761A pdb=" N ILE A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 805 No H-bonds generated for 'chain 'A' and resid 803 through 805' Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.897A pdb=" N GLU A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU A 850 " --> pdb=" O CYS A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 884 through 900 Processing helix chain 'A' and resid 906 through 914 removed outlier: 3.999A pdb=" N ASP A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 911 " --> pdb=" O GLU A 907 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 927 through 930 Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.579A pdb=" N VAL A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 965 " --> pdb=" O LYS A 961 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 998 through 1011 removed outlier: 4.984A pdb=" N THR A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1032 removed outlier: 4.629A pdb=" N SER A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1052 Processing helix chain 'A' and resid 1055 through 1067 removed outlier: 3.997A pdb=" N VAL A1063 " --> pdb=" O GLU A1060 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A1067 " --> pdb=" O ASN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1096 Processing helix chain 'A' and resid 1100 through 1104 Processing helix chain 'A' and resid 1124 through 1136 removed outlier: 3.629A pdb=" N TRP A1136 " --> pdb=" O ARG A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1230 through 1241 Processing helix chain 'A' and resid 1246 through 1252 Proline residue: A1251 - end of helix Processing helix chain 'A' and resid 1261 through 1264 No H-bonds generated for 'chain 'A' and resid 1261 through 1264' Processing helix chain 'A' and resid 1280 through 1285 removed outlier: 4.056A pdb=" N ASN A1285 " --> pdb=" O ARG A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1300 Processing helix chain 'A' and resid 1310 through 1327 removed outlier: 3.505A pdb=" N GLU A1325 " --> pdb=" O MET A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1343 No H-bonds generated for 'chain 'A' and resid 1341 through 1343' Processing helix chain 'A' and resid 1360 through 1367 Processing helix chain 'A' and resid 1369 through 1371 No H-bonds generated for 'chain 'A' and resid 1369 through 1371' Processing helix chain 'B' and resid 173 through 191 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 228 through 238 removed outlier: 4.179A pdb=" N MET B 238 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'C' and resid 177 through 197 Processing helix chain 'C' and resid 200 through 205 removed outlier: 3.594A pdb=" N ASP C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'D' and resid 174 through 194 removed outlier: 3.758A pdb=" N THR D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 217 removed outlier: 4.573A pdb=" N ILE D 207 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 209 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG D 215 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 192 removed outlier: 3.720A pdb=" N SER E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR E 192 " --> pdb=" O GLY E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 225 removed outlier: 3.637A pdb=" N GLU E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA E 220 " --> pdb=" O GLU E 216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 172 through 176 Processing sheet with id= B, first strand: chain 'A' and resid 549 through 551 Processing sheet with id= C, first strand: chain 'A' and resid 627 through 632 Processing sheet with id= D, first strand: chain 'A' and resid 807 through 809 removed outlier: 4.305A pdb=" N ILE A 807 " --> pdb=" O HIS A 814 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1153 through 1157 Processing sheet with id= F, first strand: chain 'B' and resid 194 through 196 551 hydrogen bonds defined for protein. 1533 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: 10.98 Time building geometry restraints manager: 23.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13122 1.03 - 1.23: 31 1.23 - 1.42: 5213 1.42 - 1.62: 7684 1.62 - 1.81: 119 Bond restraints: 26169 Sorted by residual: bond pdb=" C13 Y6L A9901 " pdb=" N2 Y6L A9901 " ideal model delta sigma weight residual 1.473 1.345 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C14 Y6L A9901 " pdb=" N3 Y6L A9901 " ideal model delta sigma weight residual 1.471 1.345 0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C5 Y6L A9901 " pdb=" C6 Y6L A9901 " ideal model delta sigma weight residual 1.541 1.482 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" C14 Y6L A9901 " pdb=" C15 Y6L A9901 " ideal model delta sigma weight residual 1.550 1.495 0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" C22 Y6L A9901 " pdb=" O1 Y6L A9901 " ideal model delta sigma weight residual 1.416 1.366 0.050 2.00e-02 2.50e+03 6.28e+00 ... (remaining 26164 not shown) Histogram of bond angle deviations from ideal: 59.91 - 74.73: 3 74.73 - 89.55: 0 89.55 - 104.37: 169 104.37 - 119.19: 37024 119.19 - 134.01: 10276 Bond angle restraints: 47472 Sorted by residual: angle pdb=" O Y6L A9901 " pdb=" C18 Y6L A9901 " pdb=" C22 Y6L A9901 " ideal model delta sigma weight residual 78.14 116.25 -38.11 3.00e+00 1.11e-01 1.61e+02 angle pdb=" O Y6L A9901 " pdb=" C18 Y6L A9901 " pdb=" C17 Y6L A9901 " ideal model delta sigma weight residual 152.68 123.88 28.80 3.00e+00 1.11e-01 9.22e+01 angle pdb=" N VAL A 423 " pdb=" CA VAL A 423 " pdb=" C VAL A 423 " ideal model delta sigma weight residual 112.29 108.65 3.64 9.40e-01 1.13e+00 1.50e+01 angle pdb=" C24 Y6L A9901 " pdb=" C22 Y6L A9901 " pdb=" O1 Y6L A9901 " ideal model delta sigma weight residual 113.68 124.56 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C18 Y6L A9901 " pdb=" C22 Y6L A9901 " pdb=" O1 Y6L A9901 " ideal model delta sigma weight residual 126.24 115.50 10.74 3.00e+00 1.11e-01 1.28e+01 ... (remaining 47467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 11705 29.58 - 59.16: 379 59.16 - 88.74: 37 88.74 - 118.32: 0 118.32 - 147.90: 2 Dihedral angle restraints: 12123 sinusoidal: 6811 harmonic: 5312 Sorted by residual: dihedral pdb=" CA ARG A 362 " pdb=" C ARG A 362 " pdb=" N ILE A 363 " pdb=" CA ILE A 363 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA CYS A 261 " pdb=" C CYS A 261 " pdb=" N CYS A 262 " pdb=" CA CYS A 262 " ideal model delta harmonic sigma weight residual 180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" O Y6L A9901 " pdb=" C19 Y6L A9901 " pdb=" C20 Y6L A9901 " pdb=" C21 Y6L A9901 " ideal model delta sinusoidal sigma weight residual 254.07 106.17 147.90 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 12120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1235 0.028 - 0.057: 536 0.057 - 0.085: 147 0.085 - 0.113: 69 0.113 - 0.142: 34 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CA VAL A1267 " pdb=" N VAL A1267 " pdb=" C VAL A1267 " pdb=" CB VAL A1267 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A1039 " pdb=" N ILE A1039 " pdb=" C ILE A1039 " pdb=" CB ILE A1039 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2018 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 Y6L A9901 " 0.034 2.00e-02 2.50e+03 7.06e-02 6.22e+01 pdb=" C15 Y6L A9901 " -0.067 2.00e-02 2.50e+03 pdb=" N2 Y6L A9901 " -0.088 2.00e-02 2.50e+03 pdb=" N3 Y6L A9901 " 0.106 2.00e-02 2.50e+03 pdb=" O2 Y6L A9901 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 Y6L A9901 " -0.037 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" C13 Y6L A9901 " 0.018 2.00e-02 2.50e+03 pdb=" N2 Y6L A9901 " 0.060 2.00e-02 2.50e+03 pdb=" N3 Y6L A9901 " -0.048 2.00e-02 2.50e+03 pdb=" O3 Y6L A9901 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 415 " 0.011 2.00e-02 2.50e+03 1.10e-02 4.82e+00 pdb=" CG TRP A 415 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 415 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 415 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 415 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 415 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 415 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 415 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 415 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 415 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 415 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP A 415 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 415 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 415 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 415 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 415 " -0.000 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 959 2.18 - 2.78: 52159 2.78 - 3.39: 71183 3.39 - 3.99: 92772 3.99 - 4.60: 146908 Nonbonded interactions: 363981 Sorted by model distance: nonbonded pdb=" OD1 ASP A 653 " pdb="HH22 ARG C 215 " model vdw 1.570 1.850 nonbonded pdb=" OE2 GLU A1060 " pdb="HD21 ASN A1064 " model vdw 1.611 1.850 nonbonded pdb="HD22 ASN A 88 " pdb=" O LEU A 176 " model vdw 1.616 1.850 nonbonded pdb="HH22 ARG A 341 " pdb=" O GLU B 265 " model vdw 1.634 1.850 nonbonded pdb=" H LYS A1117 " pdb=" O ARG A1121 " model vdw 1.636 1.850 ... (remaining 363976 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=0.00 max=1.00 mean=0.49 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: 1.330 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: 0.410 Extract box with map and model: 7.220 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 88.700 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.004 0.128 13026 Z= 0.263 Angle : 0.694 38.110 17566 Z= 0.347 Chirality : 0.039 0.142 2021 Planarity : 0.004 0.071 2220 Dihedral : 14.262 147.900 4993 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.21), residues: 1578 helix: 0.89 (0.18), residues: 835 sheet: -0.15 (0.63), residues: 72 loop : -1.53 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 415 HIS 0.012 0.002 HIS A 286 PHE 0.013 0.001 PHE A1310 TYR 0.014 0.001 TYR A 706 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8425 (ttp) cc_final: 0.8153 (ttm) REVERT: A 910 ASP cc_start: 0.7515 (m-30) cc_final: 0.7302 (m-30) REVERT: A 1096 GLU cc_start: 0.7376 (tt0) cc_final: 0.7059 (tp30) REVERT: A 1307 ASN cc_start: 0.7372 (m110) cc_final: 0.7164 (m-40) REVERT: A 1340 GLN cc_start: 0.7205 (mt0) cc_final: 0.6709 (mm110) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 3.0165 time to fit residues: 665.8470 Evaluate side-chains 155 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13026 Z= 0.217 Angle : 0.546 6.406 17566 Z= 0.288 Chirality : 0.039 0.144 2021 Planarity : 0.004 0.049 2220 Dihedral : 6.614 146.725 1737 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.05 % Allowed : 7.87 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.21), residues: 1578 helix: 1.02 (0.18), residues: 846 sheet: -0.12 (0.61), residues: 72 loop : -1.57 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 415 HIS 0.011 0.001 HIS A 286 PHE 0.015 0.001 PHE A1310 TYR 0.013 0.001 TYR A 706 ARG 0.006 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8416 (ttp) cc_final: 0.8170 (ttm) REVERT: A 375 MET cc_start: 0.8467 (ttt) cc_final: 0.7976 (mtp) REVERT: A 440 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: A 503 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: A 780 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 834 ASP cc_start: 0.7808 (p0) cc_final: 0.7438 (p0) REVERT: A 1096 GLU cc_start: 0.7437 (tt0) cc_final: 0.7215 (tp30) REVERT: A 1203 ARG cc_start: 0.7093 (mmt90) cc_final: 0.6175 (mmp80) REVERT: A 1247 LYS cc_start: 0.7798 (pttt) cc_final: 0.7440 (pptt) REVERT: A 1340 GLN cc_start: 0.7346 (mt0) cc_final: 0.6872 (mm110) REVERT: A 1345 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6348 (m-30) REVERT: B 250 LYS cc_start: 0.8078 (tttm) cc_final: 0.7555 (tptt) outliers start: 15 outliers final: 5 residues processed: 170 average time/residue: 2.9302 time to fit residues: 543.2771 Evaluate side-chains 163 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 499 ASN A 743 ASN A1028 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN A1353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13026 Z= 0.301 Angle : 0.599 7.128 17566 Z= 0.317 Chirality : 0.041 0.151 2021 Planarity : 0.004 0.051 2220 Dihedral : 6.874 146.465 1737 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.81 % Allowed : 9.48 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.21), residues: 1578 helix: 0.91 (0.18), residues: 843 sheet: -0.22 (0.59), residues: 72 loop : -1.59 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 415 HIS 0.011 0.002 HIS A 286 PHE 0.014 0.002 PHE A1310 TYR 0.017 0.002 TYR A 706 ARG 0.005 0.001 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.8461 (ttp) cc_final: 0.8225 (ttm) REVERT: A 282 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7145 (ttm170) REVERT: A 440 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: A 503 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: A 677 MET cc_start: 0.8889 (mmp) cc_final: 0.8660 (mmm) REVERT: A 1096 GLU cc_start: 0.7453 (tt0) cc_final: 0.7210 (tp30) REVERT: A 1247 LYS cc_start: 0.7928 (pttt) cc_final: 0.7568 (pptt) REVERT: A 1340 GLN cc_start: 0.7632 (mt0) cc_final: 0.7198 (mm110) outliers start: 26 outliers final: 10 residues processed: 176 average time/residue: 2.8716 time to fit residues: 553.9812 Evaluate side-chains 166 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1307 ASN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13026 Z= 0.273 Angle : 0.575 7.284 17566 Z= 0.303 Chirality : 0.040 0.145 2021 Planarity : 0.004 0.050 2220 Dihedral : 6.741 147.201 1737 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.74 % Allowed : 11.78 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.21 (0.21), residues: 1578 helix: 0.96 (0.18), residues: 841 sheet: -0.25 (0.59), residues: 72 loop : -1.59 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 142 HIS 0.009 0.001 HIS A 945 PHE 0.015 0.002 PHE A1310 TYR 0.014 0.002 TYR A 706 ARG 0.006 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8426 (ttp) cc_final: 0.8218 (ttm) REVERT: A 282 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7150 (ttm170) REVERT: A 375 MET cc_start: 0.8463 (mtp) cc_final: 0.8246 (mtp) REVERT: A 440 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: A 503 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: A 677 MET cc_start: 0.8864 (mmp) cc_final: 0.8660 (mmm) REVERT: A 780 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: A 790 LYS cc_start: 0.8330 (mttp) cc_final: 0.7809 (mtpp) REVERT: A 1096 GLU cc_start: 0.7438 (tt0) cc_final: 0.7176 (tp30) REVERT: A 1247 LYS cc_start: 0.7955 (pttt) cc_final: 0.7573 (pptt) REVERT: A 1340 GLN cc_start: 0.7735 (mt0) cc_final: 0.7410 (mm110) REVERT: A 1345 ASP cc_start: 0.7019 (m-30) cc_final: 0.6741 (m-30) outliers start: 25 outliers final: 11 residues processed: 178 average time/residue: 2.7533 time to fit residues: 536.2812 Evaluate side-chains 167 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1307 ASN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13026 Z= 0.279 Angle : 0.579 7.221 17566 Z= 0.306 Chirality : 0.040 0.147 2021 Planarity : 0.004 0.053 2220 Dihedral : 6.760 147.107 1737 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.02 % Allowed : 12.96 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.21 (0.21), residues: 1578 helix: 0.96 (0.18), residues: 842 sheet: -0.23 (0.60), residues: 72 loop : -1.60 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 142 HIS 0.008 0.001 HIS A 945 PHE 0.014 0.002 PHE A1310 TYR 0.016 0.002 TYR A 706 ARG 0.006 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7163 (ttm170) REVERT: A 440 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: A 503 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: A 780 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: A 790 LYS cc_start: 0.8348 (mttp) cc_final: 0.7826 (mtpp) REVERT: A 791 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6381 (mm-30) REVERT: A 1096 GLU cc_start: 0.7398 (tt0) cc_final: 0.7143 (tp30) REVERT: A 1247 LYS cc_start: 0.7961 (pttt) cc_final: 0.7591 (pptt) REVERT: A 1340 GLN cc_start: 0.7697 (mt0) cc_final: 0.7460 (mm110) REVERT: A 1345 ASP cc_start: 0.7113 (m-30) cc_final: 0.6861 (m-30) outliers start: 29 outliers final: 15 residues processed: 175 average time/residue: 2.7283 time to fit residues: 523.9020 Evaluate side-chains 171 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1307 ASN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13026 Z= 0.268 Angle : 0.573 7.270 17566 Z= 0.302 Chirality : 0.040 0.145 2021 Planarity : 0.004 0.055 2220 Dihedral : 6.742 147.164 1737 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.88 % Allowed : 14.01 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.19 (0.21), residues: 1578 helix: 0.99 (0.18), residues: 842 sheet: -0.32 (0.60), residues: 73 loop : -1.59 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 142 HIS 0.006 0.001 HIS A 286 PHE 0.015 0.002 PHE A1310 TYR 0.015 0.002 TYR A 706 ARG 0.006 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7163 (ttm170) REVERT: A 341 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7054 (mtp180) REVERT: A 440 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: A 503 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: A 780 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: A 790 LYS cc_start: 0.8370 (mttp) cc_final: 0.7840 (mtpp) REVERT: A 791 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6397 (mm-30) REVERT: A 1096 GLU cc_start: 0.7420 (tt0) cc_final: 0.7134 (tp30) REVERT: A 1247 LYS cc_start: 0.7999 (pttt) cc_final: 0.7613 (pptt) REVERT: A 1345 ASP cc_start: 0.7140 (m-30) cc_final: 0.6908 (m-30) outliers start: 27 outliers final: 15 residues processed: 173 average time/residue: 2.9681 time to fit residues: 563.9558 Evaluate side-chains 169 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1307 ASN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13026 Z= 0.209 Angle : 0.539 6.897 17566 Z= 0.283 Chirality : 0.038 0.141 2021 Planarity : 0.004 0.058 2220 Dihedral : 6.606 147.425 1737 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.88 % Allowed : 14.36 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.07 (0.21), residues: 1578 helix: 1.12 (0.19), residues: 843 sheet: -0.45 (0.63), residues: 66 loop : -1.55 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 142 HIS 0.006 0.001 HIS A 286 PHE 0.015 0.001 PHE A1310 TYR 0.012 0.001 TYR A 706 ARG 0.007 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7023 (mtp180) REVERT: A 440 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: A 503 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: A 790 LYS cc_start: 0.8361 (mttp) cc_final: 0.7830 (mtpp) REVERT: A 791 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6385 (mm-30) REVERT: A 1096 GLU cc_start: 0.7421 (tt0) cc_final: 0.7123 (tp30) REVERT: A 1247 LYS cc_start: 0.7960 (pttt) cc_final: 0.7588 (pptt) REVERT: A 1345 ASP cc_start: 0.7124 (m-30) cc_final: 0.6922 (m-30) outliers start: 27 outliers final: 17 residues processed: 178 average time/residue: 2.7633 time to fit residues: 539.3311 Evaluate side-chains 174 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1307 ASN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13026 Z= 0.279 Angle : 0.572 7.299 17566 Z= 0.301 Chirality : 0.040 0.146 2021 Planarity : 0.004 0.061 2220 Dihedral : 6.684 147.225 1737 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.95 % Allowed : 14.49 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.21), residues: 1578 helix: 1.06 (0.18), residues: 841 sheet: -0.45 (0.63), residues: 66 loop : -1.56 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 142 HIS 0.007 0.001 HIS A 683 PHE 0.020 0.002 PHE A1310 TYR 0.015 0.002 TYR A 706 ARG 0.008 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.7042 (mtp180) REVERT: A 440 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 503 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: A 790 LYS cc_start: 0.8377 (mttp) cc_final: 0.7844 (mtpp) REVERT: A 791 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6376 (mm-30) REVERT: A 1096 GLU cc_start: 0.7433 (tt0) cc_final: 0.7127 (tp30) REVERT: A 1247 LYS cc_start: 0.7999 (pttt) cc_final: 0.7615 (pptt) outliers start: 28 outliers final: 17 residues processed: 175 average time/residue: 2.8159 time to fit residues: 539.3304 Evaluate side-chains 174 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1307 ASN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13026 Z= 0.164 Angle : 0.510 6.525 17566 Z= 0.266 Chirality : 0.038 0.140 2021 Planarity : 0.004 0.050 2220 Dihedral : 6.431 147.657 1737 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.18 % Allowed : 15.33 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.17 (0.22), residues: 1578 helix: 1.31 (0.19), residues: 843 sheet: -0.30 (0.59), residues: 73 loop : -1.46 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 142 HIS 0.006 0.001 HIS A 286 PHE 0.018 0.001 PHE A1310 TYR 0.010 0.001 TYR A 706 ARG 0.008 0.000 ARG A1203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.6979 (mtp180) REVERT: A 440 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: A 790 LYS cc_start: 0.8345 (mttp) cc_final: 0.7819 (mtpp) REVERT: A 791 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6367 (mm-30) REVERT: A 1096 GLU cc_start: 0.7494 (tt0) cc_final: 0.7223 (tp30) REVERT: A 1247 LYS cc_start: 0.7930 (pttt) cc_final: 0.7547 (pptt) REVERT: A 1330 ARG cc_start: 0.7651 (ttm110) cc_final: 0.7400 (ttp-110) REVERT: B 250 LYS cc_start: 0.8111 (tttm) cc_final: 0.7607 (tptt) outliers start: 17 outliers final: 10 residues processed: 172 average time/residue: 2.8430 time to fit residues: 535.3444 Evaluate side-chains 169 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 96 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 525 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13026 Z= 0.146 Angle : 0.491 5.951 17566 Z= 0.255 Chirality : 0.037 0.138 2021 Planarity : 0.003 0.055 2220 Dihedral : 6.118 147.972 1737 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.98 % Allowed : 15.96 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.40 (0.22), residues: 1578 helix: 1.47 (0.19), residues: 847 sheet: -0.10 (0.60), residues: 73 loop : -1.33 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 142 HIS 0.006 0.001 HIS A 286 PHE 0.018 0.001 PHE A1310 TYR 0.009 0.001 TYR A 706 ARG 0.010 0.000 ARG A1203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.6991 (mtp180) REVERT: A 790 LYS cc_start: 0.8296 (mttp) cc_final: 0.7745 (mtpp) REVERT: A 1096 GLU cc_start: 0.7487 (tt0) cc_final: 0.7223 (tp30) REVERT: A 1307 ASN cc_start: 0.7299 (m110) cc_final: 0.7093 (p0) REVERT: A 1330 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7416 (ttp-110) REVERT: B 250 LYS cc_start: 0.8067 (tttm) cc_final: 0.7564 (tptt) outliers start: 14 outliers final: 10 residues processed: 175 average time/residue: 2.7548 time to fit residues: 528.5561 Evaluate side-chains 168 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 411 ASN A 743 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124564 restraints weight = 41238.811| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.85 r_work: 0.3344 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13026 Z= 0.168 Angle : 0.503 6.401 17566 Z= 0.263 Chirality : 0.038 0.138 2021 Planarity : 0.004 0.068 2220 Dihedral : 6.084 147.692 1737 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.98 % Allowed : 16.17 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.44 (0.22), residues: 1578 helix: 1.51 (0.19), residues: 847 sheet: -0.06 (0.59), residues: 73 loop : -1.33 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 142 HIS 0.006 0.001 HIS A 286 PHE 0.019 0.001 PHE A1310 TYR 0.011 0.001 TYR A 706 ARG 0.009 0.000 ARG A 852 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9565.18 seconds wall clock time: 174 minutes 7.58 seconds (10447.58 seconds total)