Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 06:09:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc7_37096/10_2023/8kc7_37096.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc7_37096/10_2023/8kc7_37096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc7_37096/10_2023/8kc7_37096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc7_37096/10_2023/8kc7_37096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc7_37096/10_2023/8kc7_37096.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc7_37096/10_2023/8kc7_37096.pdb" } resolution = 3.46 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= 0.003 sd= 0.032 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 84 5.16 5 C 9173 2.51 5 N 2402 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 976": "OD1" <-> "OD2" Residue "B ASP 978": "OD1" <-> "OD2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 14326 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3216 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4520 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 12, 'TRANS': 526} Chain breaks: 2 Chain: "D" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1474 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2762 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 3 Chain: "F" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1242 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain: "G" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1112 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 2 Time building chain proxies: 7.53, per 1000 atoms: 0.53 Number of scatterers: 14326 At special positions: 0 Unit cell: (107.36, 123.2, 154, 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 84 16.00 O 2667 8.00 N 2402 7.00 C 9173 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 Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 1.9 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 8 sheets defined 52.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.540A pdb=" N ASN A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR A 32 " --> pdb=" O VAL A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.741A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 55 No H-bonds generated for 'chain 'A' and resid 54 through 55' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.741A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.561A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.625A pdb=" N LYS A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.707A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.902A pdb=" N TYR A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 790 Processing helix chain 'B' and resid 801 through 840 Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.625A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.980A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 922 removed outlier: 4.042A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 929 Processing helix chain 'B' and resid 931 through 942 removed outlier: 4.263A pdb=" N LYS B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 957 Processing helix chain 'B' and resid 982 through 999 removed outlier: 4.038A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 3.556A pdb=" N TYR B1145 " --> pdb=" O ASN B1141 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 Processing helix chain 'B' and resid 1178 through 1184 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1233 Processing helix chain 'B' and resid 1236 through 1240 Processing helix chain 'B' and resid 1241 through 1256 Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1281 through 1293 removed outlier: 4.501A pdb=" N ILE B1285 " --> pdb=" O LYS B1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 267 Processing helix chain 'D' and resid 273 through 293 removed outlier: 3.824A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.515A pdb=" N TYR D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 345 removed outlier: 3.799A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.581A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'E' and resid 52 through 57 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.873A pdb=" N ILE E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 327 through 329 No H-bonds generated for 'chain 'E' and resid 327 through 329' Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 401 through 407 removed outlier: 3.535A pdb=" N ILE E 407 " --> pdb=" O PRO E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 450 through 452 No H-bonds generated for 'chain 'E' and resid 450 through 452' Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 543 through 577 Processing helix chain 'F' and resid 229 through 243 removed outlier: 4.960A pdb=" N THR F 240 " --> pdb=" O TRP F 236 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 Processing helix chain 'F' and resid 275 through 291 Processing helix chain 'F' and resid 299 through 313 Processing helix chain 'F' and resid 328 through 343 removed outlier: 3.564A pdb=" N LEU F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 334 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Proline residue: F 339 - end of helix Processing helix chain 'F' and resid 348 through 368 removed outlier: 3.934A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.721A pdb=" N ILE G 312 " --> pdb=" O PHE G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 removed outlier: 4.068A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS G 328 " --> pdb=" O SER G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.609A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 756 through 757 removed outlier: 3.533A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1139 through 1140 Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AA5, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA7, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA8, first strand: chain 'E' and resid 506 through 507 removed outlier: 6.112A pdb=" N GLU E 507 " --> pdb=" O GLN E 541 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 620 hydrogen bonds defined for protein. 1803 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: 4.15 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4575 1.34 - 1.46: 3201 1.46 - 1.58: 6746 1.58 - 1.70: 0 1.70 - 1.81: 124 Bond restraints: 14646 Sorted by residual: bond pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.82e+00 bond pdb=" CA THR B 968 " pdb=" CB THR B 968 " ideal model delta sigma weight residual 1.525 1.539 -0.015 8.30e-03 1.45e+04 3.06e+00 bond pdb=" C THR A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.78e+00 bond pdb=" N TYR E 505 " pdb=" CA TYR E 505 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.39e+00 bond pdb=" CA ARG E 51 " pdb=" CB ARG E 51 " ideal model delta sigma weight residual 1.528 1.551 -0.023 1.50e-02 4.44e+03 2.29e+00 ... (remaining 14641 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.06: 289 106.06 - 113.05: 7738 113.05 - 120.04: 5288 120.04 - 127.03: 6276 127.03 - 134.02: 160 Bond angle restraints: 19751 Sorted by residual: angle pdb=" N ASP B1218 " pdb=" CA ASP B1218 " pdb=" C ASP B1218 " ideal model delta sigma weight residual 114.64 108.68 5.96 1.52e+00 4.33e-01 1.54e+01 angle pdb=" CA MET F 296 " pdb=" CB MET F 296 " pdb=" CG MET F 296 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.42e+01 angle pdb=" N ARG E 51 " pdb=" CA ARG E 51 " pdb=" C ARG E 51 " ideal model delta sigma weight residual 110.33 105.63 4.70 1.29e+00 6.01e-01 1.33e+01 angle pdb=" CA GLN F 317 " pdb=" CB GLN F 317 " pdb=" CG GLN F 317 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" N TYR E 505 " pdb=" CA TYR E 505 " pdb=" C TYR E 505 " ideal model delta sigma weight residual 110.80 118.38 -7.58 2.13e+00 2.20e-01 1.26e+01 ... (remaining 19746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7647 17.93 - 35.86: 944 35.86 - 53.78: 212 53.78 - 71.71: 50 71.71 - 89.64: 18 Dihedral angle restraints: 8871 sinusoidal: 3705 harmonic: 5166 Sorted by residual: dihedral pdb=" CA ASP E 288 " pdb=" C ASP E 288 " pdb=" N PRO E 289 " pdb=" CA PRO E 289 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASP A 243 " pdb=" CB ASP A 243 " pdb=" CG ASP A 243 " pdb=" OD1 ASP A 243 " ideal model delta sinusoidal sigma weight residual -30.00 -89.98 59.98 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP B 978 " pdb=" CB ASP B 978 " pdb=" CG ASP B 978 " pdb=" OD1 ASP B 978 " ideal model delta sinusoidal sigma weight residual -30.00 -87.47 57.47 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 8868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1556 0.042 - 0.084: 436 0.084 - 0.125: 121 0.125 - 0.167: 19 0.167 - 0.209: 3 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CB ILE E 379 " pdb=" CA ILE E 379 " pdb=" CG1 ILE E 379 " pdb=" CG2 ILE E 379 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL E 561 " pdb=" CA VAL E 561 " pdb=" CG1 VAL E 561 " pdb=" CG2 VAL E 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR B1309 " pdb=" N THR B1309 " pdb=" C THR B1309 " pdb=" CB THR B1309 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2132 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 452 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO E 453 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 453 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 453 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 785 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO B 786 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 786 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 786 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 504 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C LEU E 504 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU E 504 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR E 505 " -0.013 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1446 2.75 - 3.29: 14656 3.29 - 3.82: 25191 3.82 - 4.36: 28852 4.36 - 4.90: 48699 Nonbonded interactions: 118844 Sorted by model distance: nonbonded pdb=" SG CYS E 263 " pdb=" NE2 HIS E 283 " model vdw 2.211 2.880 nonbonded pdb=" SG CYS E 263 " pdb=" CD2 HIS E 283 " model vdw 2.215 3.620 nonbonded pdb=" O PHE B 995 " pdb=" OG1 THR B 999 " model vdw 2.225 2.440 nonbonded pdb=" O HIS A 38 " pdb=" NZ LYS A 41 " model vdw 2.228 2.520 nonbonded pdb=" OD1 ASP D 235 " pdb=" OH TYR D 387 " model vdw 2.229 2.440 ... (remaining 118839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 7.960 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.520 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14646 Z= 0.179 Angle : 0.696 10.030 19751 Z= 0.366 Chirality : 0.042 0.209 2135 Planarity : 0.005 0.066 2520 Dihedral : 16.703 89.641 5525 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.93 % Allowed : 22.95 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1720 helix: 0.32 (0.17), residues: 809 sheet: -1.28 (0.51), residues: 81 loop : -1.90 (0.20), residues: 830 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 96 average time/residue: 0.2757 time to fit residues: 40.1828 Evaluate side-chains 74 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1330 time to fit residues: 3.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1274 ASN B1299 ASN E 268 GLN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14646 Z= 0.381 Angle : 0.670 10.796 19751 Z= 0.347 Chirality : 0.042 0.163 2135 Planarity : 0.004 0.056 2520 Dihedral : 4.439 24.008 1892 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.99 % Allowed : 24.32 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1720 helix: 1.14 (0.19), residues: 820 sheet: -1.17 (0.50), residues: 96 loop : -1.57 (0.22), residues: 804 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 70 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 97 average time/residue: 0.2345 time to fit residues: 36.2920 Evaluate side-chains 84 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1307 time to fit residues: 6.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN E 314 ASN E 422 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14646 Z= 0.268 Angle : 0.584 8.732 19751 Z= 0.298 Chirality : 0.040 0.149 2135 Planarity : 0.004 0.049 2520 Dihedral : 4.395 21.782 1892 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.99 % Allowed : 25.12 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1720 helix: 1.38 (0.19), residues: 821 sheet: -1.79 (0.47), residues: 102 loop : -1.44 (0.23), residues: 797 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 101 average time/residue: 0.2579 time to fit residues: 40.6652 Evaluate side-chains 80 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1310 time to fit residues: 5.2985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 ASN B1165 ASN E 376 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN G 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14646 Z= 0.347 Angle : 0.651 12.659 19751 Z= 0.331 Chirality : 0.041 0.149 2135 Planarity : 0.004 0.046 2520 Dihedral : 4.601 23.636 1892 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.36 % Allowed : 25.25 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1720 helix: 1.38 (0.18), residues: 816 sheet: -1.90 (0.47), residues: 101 loop : -1.37 (0.23), residues: 803 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 1.651 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 96 average time/residue: 0.2591 time to fit residues: 40.1533 Evaluate side-chains 82 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1458 time to fit residues: 7.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14646 Z= 0.196 Angle : 0.568 10.369 19751 Z= 0.287 Chirality : 0.039 0.148 2135 Planarity : 0.004 0.048 2520 Dihedral : 4.453 23.129 1892 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.49 % Allowed : 25.93 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1720 helix: 1.57 (0.19), residues: 815 sheet: -1.98 (0.46), residues: 101 loop : -1.36 (0.23), residues: 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.896 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 87 average time/residue: 0.2578 time to fit residues: 35.3380 Evaluate side-chains 69 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2408 time to fit residues: 4.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 14646 Z= 0.367 Angle : 0.665 9.810 19751 Z= 0.339 Chirality : 0.042 0.197 2135 Planarity : 0.004 0.046 2520 Dihedral : 4.666 24.413 1892 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.31 % Favored : 91.63 % Rotamer: Outliers : 2.24 % Allowed : 26.06 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1720 helix: 1.39 (0.18), residues: 815 sheet: -2.09 (0.48), residues: 101 loop : -1.40 (0.23), residues: 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 66 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 97 average time/residue: 0.2696 time to fit residues: 40.3745 Evaluate side-chains 83 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1363 time to fit residues: 6.9026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 140 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1247 GLN ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14646 Z= 0.257 Angle : 0.602 10.209 19751 Z= 0.305 Chirality : 0.041 0.199 2135 Planarity : 0.004 0.048 2520 Dihedral : 4.593 24.422 1892 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.06 % Allowed : 26.55 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1720 helix: 1.49 (0.18), residues: 818 sheet: -2.11 (0.48), residues: 101 loop : -1.43 (0.23), residues: 801 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 1.916 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 77 average time/residue: 0.2508 time to fit residues: 31.3935 Evaluate side-chains 72 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1947 time to fit residues: 5.4860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 105 optimal weight: 0.0470 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14646 Z= 0.200 Angle : 0.577 9.731 19751 Z= 0.291 Chirality : 0.040 0.196 2135 Planarity : 0.004 0.045 2520 Dihedral : 4.462 23.209 1892 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.56 % Allowed : 27.11 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1720 helix: 1.64 (0.19), residues: 815 sheet: -2.34 (0.47), residues: 96 loop : -1.40 (0.23), residues: 809 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.624 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 71 average time/residue: 0.2607 time to fit residues: 29.6818 Evaluate side-chains 65 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1304 time to fit residues: 3.0445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14646 Z= 0.237 Angle : 0.603 11.444 19751 Z= 0.304 Chirality : 0.040 0.196 2135 Planarity : 0.004 0.046 2520 Dihedral : 4.466 22.986 1892 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.56 % Allowed : 27.18 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1720 helix: 1.65 (0.19), residues: 814 sheet: -2.19 (0.48), residues: 101 loop : -1.41 (0.23), residues: 805 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.638 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 70 average time/residue: 0.2495 time to fit residues: 28.7174 Evaluate side-chains 65 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2966 time to fit residues: 3.5723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 14646 Z= 0.301 Angle : 0.643 12.453 19751 Z= 0.324 Chirality : 0.041 0.199 2135 Planarity : 0.004 0.045 2520 Dihedral : 4.585 24.386 1892 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.19 % Allowed : 27.55 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1720 helix: 1.55 (0.18), residues: 816 sheet: -2.22 (0.48), residues: 101 loop : -1.43 (0.23), residues: 803 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.856 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.2532 time to fit residues: 26.8392 Evaluate side-chains 63 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1382 time to fit residues: 2.5382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.048105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.038098 restraints weight = 101739.722| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.01 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14646 Z= 0.183 Angle : 0.590 12.005 19751 Z= 0.295 Chirality : 0.040 0.192 2135 Planarity : 0.004 0.048 2520 Dihedral : 4.443 23.133 1892 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.31 % Allowed : 27.36 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1720 helix: 1.65 (0.19), residues: 821 sheet: -2.30 (0.47), residues: 102 loop : -1.40 (0.23), residues: 797 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.74 seconds wall clock time: 42 minutes 51.71 seconds (2571.71 seconds total)