Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 10:58:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_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_29366/07_2023/8fpj_29366_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpj_29366/07_2023/8fpj_29366_trim_updated.pdb" } resolution = 2.74 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= 0.002 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 10.68, per 1000 atoms: 0.41 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: 21.49 Conformation dependent library (CDL) restraints added in 2.3 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: 2.40 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: 9.44 Time building geometry restraints manager: 22.12 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: 10155 29.58 - 59.16: 250 59.16 - 88.74: 34 88.74 - 118.32: 0 118.32 - 147.90: 2 Dihedral angle restraints: 10441 sinusoidal: 5129 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 10438 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: 1.580 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: 0.390 Extract box with map and model: 7.990 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 78.820 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.080 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 3.0516 time to fit residues: 673.3832 Evaluate side-chains 153 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8570 ------------------------------------------------------------------------------- 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: 0.0670 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: 0.4980 chunk 142 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.0934 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= 0.173 Angle : 0.520 5.964 17566 Z= 0.273 Chirality : 0.038 0.141 2021 Planarity : 0.004 0.048 2220 Dihedral : 6.530 146.283 1737 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.91 % 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: 0.06 (0.21), residues: 1578 helix: 1.19 (0.18), residues: 839 sheet: -0.07 (0.59), residues: 79 loop : -1.49 (0.23), residues: 660 *********************** 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 175 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 168 average time/residue: 2.9683 time to fit residues: 545.9540 Evaluate side-chains 157 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.7432 time to fit residues: 4.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 A 918 GLN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN A1353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13026 Z= 0.293 Angle : 0.581 6.913 17566 Z= 0.307 Chirality : 0.040 0.149 2021 Planarity : 0.004 0.050 2220 Dihedral : 6.732 146.734 1737 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.39 % 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: -0.15 (0.21), residues: 1578 helix: 1.00 (0.18), residues: 844 sheet: -0.21 (0.60), residues: 72 loop : -1.56 (0.23), residues: 662 *********************** 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 178 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 168 average time/residue: 3.0518 time to fit residues: 559.7547 Evaluate side-chains 159 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 1.5919 time to fit residues: 12.2081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 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: 0.5980 chunk 135 optimal weight: 5.9990 chunk 40 optimal weight: 0.0670 chunk 126 optimal weight: 2.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13026 Z= 0.191 Angle : 0.525 6.834 17566 Z= 0.275 Chirality : 0.038 0.140 2021 Planarity : 0.004 0.048 2220 Dihedral : 6.520 147.465 1737 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.39 % 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: 0.05 (0.21), residues: 1578 helix: 1.19 (0.19), residues: 845 sheet: -0.26 (0.59), residues: 72 loop : -1.50 (0.23), residues: 661 *********************** 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 177 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 170 average time/residue: 2.8487 time to fit residues: 529.9124 Evaluate side-chains 160 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.8600 time to fit residues: 5.1106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 499 ASN A 525 ASN A 743 ASN A1028 ASN ** A1162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 13026 Z= 0.352 Angle : 0.623 7.736 17566 Z= 0.330 Chirality : 0.042 0.155 2021 Planarity : 0.004 0.051 2220 Dihedral : 6.845 146.993 1737 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.88 % 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: -0.26 (0.21), residues: 1578 helix: 0.89 (0.18), residues: 843 sheet: -0.27 (0.59), residues: 72 loop : -1.58 (0.23), residues: 663 *********************** 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 189 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 178 average time/residue: 2.8211 time to fit residues: 553.3886 Evaluate side-chains 162 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 2.219 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.6644 time to fit residues: 9.2046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 146 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 13026 Z= 0.151 Angle : 0.507 6.683 17566 Z= 0.264 Chirality : 0.037 0.140 2021 Planarity : 0.003 0.047 2220 Dihedral : 6.383 147.710 1737 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.25 % 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: 0.15 (0.22), residues: 1578 helix: 1.28 (0.19), residues: 846 sheet: -0.21 (0.59), residues: 72 loop : -1.47 (0.23), residues: 660 *********************** 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 173 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 169 average time/residue: 2.7958 time to fit residues: 519.7889 Evaluate side-chains 161 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 2.125 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.7944 time to fit residues: 4.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7984 moved from start: 0.1829 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= 0.279 Angle : 0.575 7.425 17566 Z= 0.302 Chirality : 0.040 0.150 2021 Planarity : 0.004 0.056 2220 Dihedral : 6.625 147.308 1737 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 1.53 % 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: -0.03 (0.21), residues: 1578 helix: 1.12 (0.19), residues: 844 sheet: -0.22 (0.59), residues: 72 loop : -1.53 (0.23), residues: 662 *********************** 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 176 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 170 average time/residue: 2.7781 time to fit residues: 519.1163 Evaluate side-chains 164 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 2.3793 time to fit residues: 8.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 13026 Z= 0.305 Angle : 0.601 7.521 17566 Z= 0.316 Chirality : 0.041 0.148 2021 Planarity : 0.004 0.048 2220 Dihedral : 6.775 147.172 1737 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.46 % 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: -0.20 (0.21), residues: 1578 helix: 0.98 (0.18), residues: 842 sheet: -0.38 (0.59), residues: 73 loop : -1.58 (0.23), residues: 663 *********************** 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 176 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 2.305 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 170 average time/residue: 2.7894 time to fit residues: 522.7070 Evaluate side-chains 167 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 2.2935 time to fit residues: 10.4316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4752 > 50: distance: 324 - 336: 12.846 distance: 336 - 337: 8.655 distance: 336 - 347: 12.953 distance: 337 - 338: 12.772 distance: 337 - 340: 37.751 distance: 337 - 348: 34.699 distance: 338 - 339: 17.392 distance: 338 - 356: 6.255 distance: 340 - 341: 6.560 distance: 340 - 349: 4.288 distance: 340 - 350: 11.309 distance: 341 - 342: 23.406 distance: 341 - 343: 8.753 distance: 342 - 344: 12.023 distance: 342 - 351: 10.872 distance: 343 - 345: 15.936 distance: 343 - 352: 8.902 distance: 344 - 346: 14.069 distance: 344 - 353: 11.047 distance: 345 - 346: 11.989 distance: 345 - 354: 11.654 distance: 346 - 355: 12.314 distance: 356 - 357: 17.422 distance: 356 - 365: 6.501 distance: 357 - 358: 23.935 distance: 357 - 360: 26.282 distance: 357 - 366: 17.197 distance: 358 - 359: 14.878 distance: 358 - 373: 42.066 distance: 360 - 361: 49.075 distance: 360 - 367: 17.849 distance: 360 - 368: 23.324 distance: 361 - 362: 12.179 distance: 361 - 369: 11.376 distance: 361 - 370: 35.332 distance: 362 - 363: 26.459 distance: 362 - 364: 5.754 distance: 364 - 372: 7.928 distance: 373 - 374: 42.401 distance: 374 - 375: 16.450 distance: 374 - 378: 52.989 distance: 374 - 379: 49.965 distance: 375 - 376: 39.080 distance: 375 - 380: 36.923 distance: 380 - 381: 25.474 distance: 380 - 389: 17.322 distance: 381 - 382: 21.329 distance: 381 - 384: 14.996 distance: 381 - 390: 14.572 distance: 382 - 383: 11.801 distance: 382 - 402: 10.329 distance: 384 - 385: 21.614 distance: 384 - 391: 29.966 distance: 384 - 392: 18.141 distance: 385 - 386: 12.667 distance: 385 - 393: 11.260 distance: 385 - 394: 15.521 distance: 386 - 387: 14.404 distance: 386 - 395: 7.418 distance: 386 - 396: 12.058 distance: 387 - 388: 5.300 distance: 387 - 397: 19.116 distance: 387 - 398: 4.425 distance: 388 - 399: 7.409 distance: 388 - 401: 3.522 distance: 402 - 403: 34.543 distance: 402 - 413: 18.122 distance: 403 - 404: 9.812 distance: 403 - 406: 7.152 distance: 403 - 414: 30.553 distance: 404 - 422: 69.378 distance: 406 - 407: 22.433 distance: 406 - 415: 28.429 distance: 406 - 416: 10.694 distance: 407 - 408: 20.213 distance: 407 - 409: 18.581 distance: 408 - 410: 10.725 distance: 408 - 417: 3.922 distance: 409 - 411: 12.253 distance: 409 - 418: 4.378 distance: 410 - 412: 13.652 distance: 410 - 419: 4.249 distance: 411 - 412: 7.685 distance: 411 - 420: 6.252 distance: 422 - 423: 11.606 distance: 423 - 424: 15.311 distance: 423 - 426: 22.239 distance: 423 - 431: 10.680 distance: 424 - 425: 30.307 distance: 424 - 436: 33.944 distance: 426 - 427: 4.753 distance: 426 - 432: 32.010 distance: 426 - 433: 9.507 distance: 427 - 428: 7.467 distance: 427 - 429: 34.207 distance: 429 - 434: 12.861 distance: 429 - 435: 18.652 distance: 436 - 437: 9.763 distance: 436 - 448: 13.294 distance: 437 - 438: 10.113 distance: 437 - 440: 9.484 distance: 437 - 449: 16.578 distance: 438 - 439: 4.696 distance: 438 - 457: 13.037 distance: 440 - 441: 5.671 distance: 440 - 450: 13.808 distance: 440 - 451: 3.459 distance: 441 - 442: 12.879 distance: 441 - 443: 7.444 distance: 442 - 444: 18.642 distance: 442 - 452: 16.214 distance: 443 - 445: 14.155 distance: 444 - 446: 7.071 distance: 444 - 454: 12.374 distance: 445 - 446: 17.059 distance: 445 - 455: 8.119 distance: 446 - 447: 13.572 distance: 447 - 456: 7.996 distance: 457 - 466: 15.875 distance: 458 - 459: 15.199 distance: 458 - 461: 29.397 distance: 458 - 467: 15.325 distance: 459 - 460: 24.716 distance: 461 - 462: 18.882 distance: 461 - 468: 12.200 distance: 461 - 469: 52.251 distance: 462 - 463: 31.252 distance: 462 - 470: 18.411 distance: 462 - 471: 28.036 distance: 463 - 464: 35.700 distance: 463 - 472: 14.132 distance: 463 - 473: 12.474 distance: 464 - 465: 24.362 distance: 464 - 474: 13.334 distance: 464 - 475: 25.074 distance: 465 - 476: 9.729 distance: 465 - 477: 6.770 distance: 465 - 478: 9.735 distance: 479 - 480: 12.394 distance: 479 - 487: 9.357 distance: 480 - 481: 15.402 distance: 480 - 483: 26.882 distance: 480 - 488: 9.425 distance: 481 - 482: 20.341 distance: 481 - 498: 25.073 distance: 482 - 535: 32.740 distance: 483 - 484: 18.675 distance: 483 - 489: 20.408 distance: 483 - 490: 13.532 distance: 484 - 485: 12.296 distance: 484 - 491: 11.873 distance: 485 - 492: 15.666 distance: 485 - 493: 9.395 distance: 485 - 494: 18.219 distance: 486 - 495: 10.648 distance: 486 - 496: 8.897 distance: 486 - 497: 7.505 distance: 498 - 499: 7.802 distance: 498 - 505: 30.079 distance: 499 - 500: 9.590 distance: 499 - 502: 13.330 distance: 499 - 506: 15.597 distance: 500 - 501: 29.205 distance: 500 - 514: 13.115 distance: 501 - 553: 20.805 distance: 502 - 503: 13.077 distance: 502 - 504: 17.782 distance: 502 - 507: 20.650 distance: 503 - 508: 12.621 distance: 503 - 509: 14.007 distance: 503 - 510: 5.602 distance: 504 - 511: 5.295 distance: 504 - 512: 15.153 distance: 504 - 513: 11.367