Starting phenix.real_space_refine on Sat Aug 3 13:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/08_2024/8k77_36935.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/08_2024/8k77_36935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/08_2024/8k77_36935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/08_2024/8k77_36935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/08_2024/8k77_36935.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k77_36935/08_2024/8k77_36935.cif" } resolution = 3.11 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= 0.000 sd= 1.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5294 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A ASP 479": "OD1" <-> "OD2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1086": "OD1" <-> "OD2" Residue "B ASP 1089": "OD1" <-> "OD2" Residue "B ASP 1099": "OD1" <-> "OD2" Residue "B TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1171": "OD1" <-> "OD2" Residue "B TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1190": "OE1" <-> "OE2" Residue "B TYR 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1283": "OE1" <-> "OE2" Residue "B PHE 1284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1293": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2, 'VLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.61, per 1000 atoms: 0.68 Number of scatterers: 8192 At special positions: 0 Unit cell: (84.66, 83.83, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1489 8.00 N 1362 7.00 C 5294 6.00 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG C 1 " - " ASN A 573 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.4 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 43.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.700A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Proline residue: A 191 - end of helix removed outlier: 4.108A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 4.435A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 250 Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.491A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.568A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 284 No H-bonds generated for 'chain 'A' and resid 283 through 284' Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.711A pdb=" N LYS A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.826A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.725A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.669A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 593 through 619 removed outlier: 3.729A pdb=" N VAL A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.530A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.836A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.791A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 Processing helix chain 'A' and resid 712 through 731 removed outlier: 4.000A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.888A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.639A pdb=" N LEU B 958 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 485 through 492 current: chain 'A' and resid 514 through 527 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 514 through 527 current: chain 'B' and resid 1142 through 1144 Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884 removed outlier: 3.720A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 887 through 890 current: chain 'B' and resid 914 through 917 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 917 current: chain 'B' and resid 1015 through 1021 removed outlier: 3.856A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900 removed outlier: 7.659A pdb=" N MET B1054 " --> pdb=" O CYS B 967 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 967 " --> pdb=" O MET B1054 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS B1056 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 965 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR B 963 " --> pdb=" O LEU B 978 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 978 " --> pdb=" O THR B 963 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP B 974 " --> pdb=" O CYS B 967 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA5, first strand: chain 'B' and resid 1122 through 1125 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1134 through 1137 current: chain 'B' and resid 1179 through 1186 removed outlier: 5.618A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1189 through 1194 current: chain 'B' and resid 1232 through 1240 removed outlier: 27.341A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.656A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.969A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1071 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: 3.13 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 2 1.18 - 1.34: 2535 1.34 - 1.49: 2386 1.49 - 1.65: 3387 1.65 - 1.81: 76 Bond restraints: 8386 Sorted by residual: bond pdb=" CG PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 1.503 1.158 0.345 3.40e-02 8.65e+02 1.03e+02 bond pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 1.492 1.021 0.471 5.00e-02 4.00e+02 8.89e+01 bond pdb=" C6 VLX A 803 " pdb=" N1 VLX A 803 " ideal model delta sigma weight residual 1.351 1.500 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C9 VLX A 803 " pdb=" N2 VLX A 803 " ideal model delta sigma weight residual 1.339 1.448 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" N PRO A 343 " pdb=" CA PRO A 343 " ideal model delta sigma weight residual 1.471 1.525 -0.054 1.32e-02 5.74e+03 1.67e+01 ... (remaining 8381 not shown) Histogram of bond angle deviations from ideal: 75.32 - 96.25: 2 96.25 - 117.17: 5864 117.17 - 138.10: 5472 138.10 - 159.03: 0 159.03 - 179.95: 1 Bond angle restraints: 11339 Sorted by residual: angle pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO A 343 " pdb=" CD PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 103.20 76.47 26.73 1.50e+00 4.44e-01 3.18e+02 angle pdb=" CA PRO A 343 " pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 104.50 75.32 29.18 1.90e+00 2.77e-01 2.36e+02 angle pdb=" CA PRO A 343 " pdb=" N PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 112.00 101.62 10.38 1.40e+00 5.10e-01 5.50e+01 angle pdb=" N PRO A 343 " pdb=" CA PRO A 343 " pdb=" C PRO A 343 " ideal model delta sigma weight residual 113.84 120.10 -6.26 1.30e+00 5.92e-01 2.32e+01 ... (remaining 11334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4257 16.65 - 33.31: 502 33.31 - 49.96: 161 49.96 - 66.62: 34 66.62 - 83.27: 15 Dihedral angle restraints: 4969 sinusoidal: 2046 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ASP A 528 " pdb=" CB ASP A 528 " pdb=" CG ASP A 528 " pdb=" OD1 ASP A 528 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASP A 620 " pdb=" CB ASP A 620 " pdb=" CG ASP A 620 " pdb=" OD1 ASP A 620 " ideal model delta sinusoidal sigma weight residual -30.00 -84.03 54.03 1 2.00e+01 2.50e-03 9.90e+00 dihedral pdb=" CG ARG B 996 " pdb=" CD ARG B 996 " pdb=" NE ARG B 996 " pdb=" CZ ARG B 996 " ideal model delta sinusoidal sigma weight residual 90.00 132.49 -42.49 2 1.50e+01 4.44e-03 9.73e+00 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1217 0.113 - 0.226: 26 0.226 - 0.338: 1 0.338 - 0.451: 0 0.451 - 0.564: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.53e+00 ... (remaining 1242 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 441 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 342 " -0.071 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO A 343 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 343 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C PRO A 343 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO A 343 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 344 " 0.015 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 223 2.71 - 3.26: 8033 3.26 - 3.80: 13167 3.80 - 4.35: 16905 4.35 - 4.90: 28823 Nonbonded interactions: 67151 Sorted by model distance: nonbonded pdb=" O GLY B1129 " pdb=" OG SER B1207 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR B 934 " pdb=" O GLU B 939 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG B 903 " pdb=" OH TYR B 905 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.263 3.040 ... (remaining 67146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.471 8386 Z= 0.545 Angle : 0.987 73.852 11339 Z= 0.450 Chirality : 0.047 0.564 1245 Planarity : 0.005 0.106 1428 Dihedral : 16.518 83.272 3103 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.80 (0.27), residues: 1006 helix: 1.90 (0.26), residues: 407 sheet: 0.20 (0.33), residues: 243 loop : -0.79 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.003 0.001 HIS A 494 PHE 0.019 0.001 PHE A 342 TYR 0.016 0.001 TYR A 306 ARG 0.014 0.001 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2482 time to fit residues: 34.6716 Evaluate side-chains 105 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 434 ASN A 504 GLN A 568 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 988 GLN B1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 8386 Z= 0.160 Angle : 0.472 5.893 11339 Z= 0.257 Chirality : 0.043 0.418 1245 Planarity : 0.003 0.062 1428 Dihedral : 5.591 52.919 1226 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.93 % Allowed : 17.29 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.23 (0.27), residues: 1006 helix: 2.43 (0.26), residues: 412 sheet: 0.21 (0.33), residues: 243 loop : -0.69 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.010 0.001 PHE A 459 TYR 0.011 0.001 TYR A 306 ARG 0.002 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 442 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 535 TYR cc_start: 0.8292 (t80) cc_final: 0.7934 (t80) REVERT: B 903 ARG cc_start: 0.7520 (mmm160) cc_final: 0.7211 (mmm160) REVERT: B 1058 ASP cc_start: 0.7527 (m-30) cc_final: 0.7262 (m-30) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 0.2141 time to fit residues: 34.3009 Evaluate side-chains 113 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 62 optimal weight: 0.0000 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 354 GLN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1022 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8386 Z= 0.374 Angle : 0.580 5.616 11339 Z= 0.312 Chirality : 0.047 0.338 1245 Planarity : 0.004 0.045 1428 Dihedral : 5.927 46.994 1226 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.32 % Allowed : 15.47 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.88 (0.27), residues: 1006 helix: 2.15 (0.26), residues: 408 sheet: 0.05 (0.33), residues: 236 loop : -0.86 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.015 0.002 PHE A 277 TYR 0.024 0.002 TYR A 306 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6963 (ttp-110) REVERT: A 442 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 523 SER cc_start: 0.8733 (m) cc_final: 0.8278 (p) REVERT: A 741 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7924 (tp) REVERT: B 1058 ASP cc_start: 0.7575 (m-30) cc_final: 0.7332 (m-30) REVERT: B 1085 LYS cc_start: 0.7736 (tppp) cc_final: 0.7275 (tppt) outliers start: 38 outliers final: 26 residues processed: 141 average time/residue: 0.2169 time to fit residues: 41.5322 Evaluate side-chains 128 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1242 ASN Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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: 64.6141 > 50: distance: 51 - 55: 22.497 distance: 55 - 56: 7.989 distance: 56 - 57: 10.118 distance: 57 - 58: 18.966 distance: 57 - 59: 30.128 distance: 59 - 60: 10.128 distance: 60 - 61: 19.106 distance: 60 - 63: 10.195 distance: 61 - 62: 16.477 distance: 61 - 67: 10.063 distance: 63 - 64: 12.076 distance: 63 - 65: 8.406 distance: 64 - 66: 13.926 distance: 67 - 68: 12.021 distance: 68 - 69: 32.659 distance: 68 - 71: 8.494 distance: 69 - 70: 34.544 distance: 69 - 75: 24.564 distance: 71 - 72: 14.617 distance: 72 - 73: 24.895 distance: 72 - 74: 36.546 distance: 75 - 76: 32.063 distance: 76 - 77: 39.755 distance: 76 - 79: 31.583 distance: 77 - 78: 14.443 distance: 77 - 84: 19.732 distance: 79 - 80: 15.094 distance: 80 - 81: 19.140 distance: 81 - 82: 20.564 distance: 82 - 83: 27.653 distance: 84 - 85: 23.031 distance: 85 - 86: 27.768 distance: 85 - 88: 40.635 distance: 86 - 87: 18.559 distance: 86 - 92: 24.654 distance: 88 - 89: 39.876 distance: 89 - 90: 12.424 distance: 89 - 91: 40.707 distance: 92 - 93: 8.508 distance: 93 - 94: 15.533 distance: 93 - 96: 17.959 distance: 94 - 95: 17.768 distance: 94 - 103: 17.132 distance: 96 - 97: 10.361 distance: 97 - 98: 28.228 distance: 97 - 99: 10.272 distance: 98 - 100: 19.136 distance: 99 - 101: 19.580 distance: 100 - 102: 26.175 distance: 101 - 102: 19.428 distance: 103 - 104: 8.947 distance: 104 - 105: 22.165 distance: 104 - 107: 13.661 distance: 105 - 106: 9.115 distance: 105 - 117: 18.610 distance: 107 - 108: 26.507 distance: 108 - 109: 37.817 distance: 108 - 110: 22.081 distance: 109 - 111: 15.256 distance: 110 - 112: 23.986 distance: 110 - 113: 13.793 distance: 111 - 112: 19.267 distance: 112 - 114: 25.766 distance: 113 - 115: 13.231 distance: 114 - 116: 14.281 distance: 115 - 116: 20.350 distance: 117 - 118: 34.300 distance: 118 - 119: 38.202 distance: 119 - 120: 26.237 distance: 119 - 121: 9.945 distance: 121 - 122: 19.619 distance: 122 - 123: 8.845 distance: 122 - 125: 26.278 distance: 123 - 124: 31.651 distance: 123 - 129: 25.229 distance: 125 - 126: 38.555 distance: 126 - 127: 35.476 distance: 126 - 128: 42.171 distance: 129 - 130: 31.352 distance: 130 - 131: 14.899 distance: 130 - 133: 25.683 distance: 131 - 132: 3.494 distance: 131 - 141: 33.089 distance: 133 - 134: 9.262 distance: 134 - 135: 24.058 distance: 134 - 136: 25.317 distance: 135 - 137: 14.367 distance: 136 - 138: 43.663 distance: 137 - 139: 41.082 distance: 138 - 139: 40.768 distance: 139 - 140: 19.424