Starting phenix.real_space_refine on Thu Jun 12 21:13:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc7_37096/06_2025/8kc7_37096.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc7_37096/06_2025/8kc7_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/cci-nas-00/data/ceres_data/8kc7_37096/06_2025/8kc7_37096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc7_37096/06_2025/8kc7_37096.map" model { file = "/net/cci-nas-00/data/ceres_data/8kc7_37096/06_2025/8kc7_37096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc7_37096/06_2025/8kc7_37096.cif" } 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. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.46, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 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: 3.49 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: 1.28 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: 4.33 Time building geometry restraints manager: 4.20 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: 0.00 - 2.01: 19343 2.01 - 4.01: 304 4.01 - 6.02: 66 6.02 - 8.02: 27 8.02 - 10.03: 11 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 3.480 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 3.040 nonbonded pdb=" O HIS A 38 " pdb=" NZ LYS A 41 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASP D 235 " pdb=" OH TYR D 387 " model vdw 2.229 3.040 ... (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 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: 2.300 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: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 32.770 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- 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= 0.148 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 966 HIS 0.003 0.001 HIS B1252 PHE 0.014 0.001 PHE G 336 TYR 0.020 0.001 TYR D 299 ARG 0.005 0.000 ARG B1009 Details of bonding type rmsd hydrogen bonds : bond 0.15407 ( 620) hydrogen bonds : angle 5.85265 ( 1803) covalent geometry : bond 0.00277 (14646) covalent geometry : angle 0.69563 (19751) *********************** 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 to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 841 MET cc_start: 0.6433 (ptt) cc_final: 0.6167 (ptt) REVERT: B 970 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.3899 (tptt) REVERT: E 560 MET cc_start: 0.8003 (tpt) cc_final: 0.7707 (mmm) outliers start: 15 outliers final: 3 residues processed: 96 average time/residue: 0.2694 time to fit residues: 39.2028 Evaluate side-chains 75 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.3980 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 961 ASN B1274 ASN E 268 GLN ** E 448 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.048478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.038512 restraints weight = 104938.862| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.86 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14646 Z= 0.246 Angle : 0.648 12.482 19751 Z= 0.334 Chirality : 0.042 0.155 2135 Planarity : 0.004 0.058 2520 Dihedral : 5.006 55.315 1900 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.80 % Allowed : 22.70 % Favored : 75.50 % 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: -0.37 (0.21), residues: 1720 helix: 1.12 (0.18), residues: 814 sheet: -1.03 (0.52), residues: 96 loop : -1.63 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 966 HIS 0.005 0.001 HIS B1252 PHE 0.032 0.002 PHE B 977 TYR 0.021 0.002 TYR A 145 ARG 0.007 0.001 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 620) hydrogen bonds : angle 4.57472 ( 1803) covalent geometry : bond 0.00526 (14646) covalent geometry : angle 0.64762 (19751) *********************** 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 99 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8219 (m) cc_final: 0.8000 (p) REVERT: A 204 MET cc_start: 0.8293 (ptt) cc_final: 0.8086 (ptt) REVERT: A 306 MET cc_start: 0.9118 (ttt) cc_final: 0.8853 (ttm) REVERT: B 844 ASN cc_start: 0.9680 (m-40) cc_final: 0.9172 (p0) REVERT: B 960 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 970 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.4787 (tptt) REVERT: E 438 MET cc_start: 0.8828 (ppp) cc_final: 0.7903 (ppp) outliers start: 29 outliers final: 16 residues processed: 94 average time/residue: 0.2453 time to fit residues: 36.7568 Evaluate side-chains 83 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1258 THR Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 331 ASN ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.049483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.039513 restraints weight = 103951.684| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.94 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14646 Z= 0.120 Angle : 0.546 8.878 19751 Z= 0.277 Chirality : 0.039 0.149 2135 Planarity : 0.004 0.054 2520 Dihedral : 4.782 54.260 1899 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.80 % Allowed : 22.95 % Favored : 75.25 % 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: 1.45 (0.19), residues: 816 sheet: -1.39 (0.52), residues: 98 loop : -1.48 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 966 HIS 0.004 0.001 HIS A 188 PHE 0.021 0.001 PHE B 977 TYR 0.023 0.001 TYR A 3 ARG 0.004 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 620) hydrogen bonds : angle 4.29496 ( 1803) covalent geometry : bond 0.00259 (14646) covalent geometry : angle 0.54594 (19751) *********************** 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 100 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8197 (m) cc_final: 0.7987 (p) REVERT: B 844 ASN cc_start: 0.9649 (m-40) cc_final: 0.9131 (p0) REVERT: B 970 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.4784 (tptt) REVERT: E 438 MET cc_start: 0.8916 (ppp) cc_final: 0.7954 (ppp) REVERT: G 560 MET cc_start: 0.8395 (mpp) cc_final: 0.7933 (mpp) outliers start: 29 outliers final: 14 residues processed: 96 average time/residue: 0.2452 time to fit residues: 37.2272 Evaluate side-chains 83 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1258 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 127 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 E 314 ASN E 541 GLN ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.048565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.038600 restraints weight = 104095.344| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.86 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14646 Z= 0.175 Angle : 0.572 8.410 19751 Z= 0.291 Chirality : 0.040 0.152 2135 Planarity : 0.004 0.050 2520 Dihedral : 4.794 53.020 1899 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.36 % Allowed : 23.38 % Favored : 74.25 % 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: 0.02 (0.21), residues: 1720 helix: 1.51 (0.19), residues: 815 sheet: -1.53 (0.50), residues: 102 loop : -1.40 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 492 HIS 0.004 0.001 HIS A 49 PHE 0.028 0.001 PHE B 977 TYR 0.024 0.001 TYR A 3 ARG 0.011 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 620) hydrogen bonds : angle 4.26671 ( 1803) covalent geometry : bond 0.00380 (14646) covalent geometry : angle 0.57160 (19751) *********************** 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 106 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 848 ASN cc_start: 0.9733 (OUTLIER) cc_final: 0.9201 (p0) REVERT: B 970 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.4842 (tptt) REVERT: D 401 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6413 (tmm) REVERT: E 560 MET cc_start: 0.8479 (tpt) cc_final: 0.7985 (tpt) REVERT: G 560 MET cc_start: 0.8431 (mpp) cc_final: 0.7982 (mpp) outliers start: 38 outliers final: 22 residues processed: 99 average time/residue: 0.2386 time to fit residues: 37.9597 Evaluate side-chains 93 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1258 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 114 optimal weight: 0.0050 chunk 136 optimal weight: 0.8980 chunk 121 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.0870 overall best weight: 0.3950 ------------------------------------------------------------------------------- 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** E 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.050065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.040167 restraints weight = 103833.138| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.92 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14646 Z= 0.096 Angle : 0.523 11.989 19751 Z= 0.263 Chirality : 0.038 0.158 2135 Planarity : 0.003 0.052 2520 Dihedral : 4.584 52.700 1899 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.05 % Allowed : 23.51 % Favored : 74.44 % 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: 0.15 (0.21), residues: 1720 helix: 1.63 (0.19), residues: 831 sheet: -1.61 (0.50), residues: 97 loop : -1.40 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 966 HIS 0.004 0.001 HIS A 49 PHE 0.026 0.001 PHE B 977 TYR 0.027 0.001 TYR A 3 ARG 0.006 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 620) hydrogen bonds : angle 4.07110 ( 1803) covalent geometry : bond 0.00197 (14646) covalent geometry : angle 0.52316 (19751) *********************** 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 105 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 970 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.5042 (tptt) REVERT: E 438 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.7785 (ppp) REVERT: G 560 MET cc_start: 0.8467 (mpp) cc_final: 0.8112 (mpp) outliers start: 33 outliers final: 18 residues processed: 96 average time/residue: 0.2344 time to fit residues: 35.9989 Evaluate side-chains 87 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 45 optimal weight: 0.0670 chunk 111 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- 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 E 314 ASN F 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.049390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.039413 restraints weight = 104522.284| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.97 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14646 Z= 0.118 Angle : 0.537 11.965 19751 Z= 0.267 Chirality : 0.039 0.162 2135 Planarity : 0.003 0.048 2520 Dihedral : 4.490 50.416 1899 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.87 % Allowed : 24.13 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1720 helix: 1.74 (0.19), residues: 824 sheet: -1.61 (0.50), residues: 97 loop : -1.33 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 966 HIS 0.004 0.001 HIS B1252 PHE 0.028 0.001 PHE B 977 TYR 0.025 0.001 TYR A 3 ARG 0.003 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 620) hydrogen bonds : angle 4.03677 ( 1803) covalent geometry : bond 0.00256 (14646) covalent geometry : angle 0.53710 (19751) *********************** 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 96 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 1.802 Fit side-chains REVERT: B 970 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.5032 (tptt) REVERT: B 1303 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7466 (mm) REVERT: E 438 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.7707 (ppp) REVERT: E 560 MET cc_start: 0.8381 (tpt) cc_final: 0.7871 (tpt) REVERT: F 296 MET cc_start: 0.8838 (pmm) cc_final: 0.8361 (pmm) REVERT: G 560 MET cc_start: 0.8484 (mpp) cc_final: 0.8206 (mpp) outliers start: 30 outliers final: 17 residues processed: 91 average time/residue: 0.2371 time to fit residues: 35.1704 Evaluate side-chains 86 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1303 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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** B 974 GLN B1165 ASN E 325 ASN F 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.047626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.037787 restraints weight = 105206.268| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.77 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2469 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= 0.225 Angle : 0.634 11.592 19751 Z= 0.321 Chirality : 0.041 0.171 2135 Planarity : 0.004 0.049 2520 Dihedral : 4.846 54.742 1899 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.55 % Allowed : 24.00 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1720 helix: 1.58 (0.19), residues: 820 sheet: -1.54 (0.54), residues: 92 loop : -1.32 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1223 HIS 0.005 0.001 HIS A 49 PHE 0.038 0.002 PHE B 977 TYR 0.025 0.002 TYR A 3 ARG 0.005 0.000 ARG E 496 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 620) hydrogen bonds : angle 4.28309 ( 1803) covalent geometry : bond 0.00485 (14646) covalent geometry : angle 0.63443 (19751) *********************** 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 107 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 1.629 Fit side-chains REVERT: B 848 ASN cc_start: 0.9732 (OUTLIER) cc_final: 0.9237 (p0) REVERT: B 970 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.5173 (tptt) REVERT: E 438 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: F 296 MET cc_start: 0.8946 (pmm) cc_final: 0.8733 (pmm) outliers start: 41 outliers final: 24 residues processed: 100 average time/residue: 0.2193 time to fit residues: 36.4682 Evaluate side-chains 91 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.048700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.038873 restraints weight = 102679.477| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.78 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14646 Z= 0.115 Angle : 0.566 11.893 19751 Z= 0.281 Chirality : 0.039 0.155 2135 Planarity : 0.003 0.052 2520 Dihedral : 4.710 53.193 1899 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.74 % Allowed : 24.88 % Favored : 73.38 % 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: 0.21 (0.21), residues: 1720 helix: 1.69 (0.19), residues: 819 sheet: -1.72 (0.50), residues: 97 loop : -1.31 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 966 HIS 0.004 0.001 HIS B1252 PHE 0.028 0.001 PHE B 977 TYR 0.027 0.001 TYR A 3 ARG 0.002 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 620) hydrogen bonds : angle 4.09693 ( 1803) covalent geometry : bond 0.00252 (14646) covalent geometry : angle 0.56576 (19751) *********************** 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 93 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.883 Fit side-chains REVERT: B 970 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.5211 (tptt) REVERT: E 438 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7806 (ppp) REVERT: G 560 MET cc_start: 0.8285 (mpp) cc_final: 0.8008 (mpp) outliers start: 28 outliers final: 21 residues processed: 89 average time/residue: 0.2323 time to fit residues: 34.1519 Evaluate side-chains 86 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 170 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 F 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.048071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.038290 restraints weight = 104019.467| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.71 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2455 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= 0.173 Angle : 0.594 11.384 19751 Z= 0.296 Chirality : 0.040 0.160 2135 Planarity : 0.004 0.049 2520 Dihedral : 4.710 53.484 1899 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.80 % Allowed : 24.56 % Favored : 73.63 % 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: 0.25 (0.21), residues: 1720 helix: 1.68 (0.19), residues: 819 sheet: -1.55 (0.54), residues: 91 loop : -1.26 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 966 HIS 0.004 0.001 HIS B1252 PHE 0.037 0.001 PHE B 977 TYR 0.027 0.001 TYR A 3 ARG 0.002 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 620) hydrogen bonds : angle 4.15411 ( 1803) covalent geometry : bond 0.00379 (14646) covalent geometry : angle 0.59379 (19751) *********************** 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 94 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 1.692 Fit side-chains REVERT: B 848 ASN cc_start: 0.9729 (OUTLIER) cc_final: 0.9253 (p0) REVERT: B 970 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.5229 (tptt) REVERT: E 438 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7816 (ppp) REVERT: F 296 MET cc_start: 0.8829 (pmm) cc_final: 0.8606 (pmm) outliers start: 29 outliers final: 24 residues processed: 90 average time/residue: 0.2321 time to fit residues: 34.7069 Evaluate side-chains 91 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 14 optimal weight: 0.0970 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 144 optimal weight: 0.0040 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.048186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.038288 restraints weight = 103584.141| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.83 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 14646 Z= 0.195 Angle : 0.893 59.200 19751 Z= 0.510 Chirality : 0.044 0.802 2135 Planarity : 0.005 0.124 2520 Dihedral : 4.718 53.375 1899 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.68 % Allowed : 24.69 % Favored : 73.63 % Cbeta Deviations : 0.12 % 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: 0.26 (0.21), residues: 1720 helix: 1.70 (0.19), residues: 819 sheet: -1.56 (0.54), residues: 91 loop : -1.27 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 966 HIS 0.004 0.001 HIS B1252 PHE 0.035 0.001 PHE B 977 TYR 0.032 0.001 TYR F 373 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 620) hydrogen bonds : angle 4.15797 ( 1803) covalent geometry : bond 0.00426 (14646) covalent geometry : angle 0.89255 (19751) ********************** 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 91 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 2.077 Fit side-chains REVERT: B 848 ASN cc_start: 0.9736 (OUTLIER) cc_final: 0.9258 (p0) REVERT: B 970 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.5167 (tptt) REVERT: E 438 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7823 (ppp) REVERT: F 296 MET cc_start: 0.8833 (pmm) cc_final: 0.8612 (pmm) outliers start: 27 outliers final: 24 residues processed: 87 average time/residue: 0.2347 time to fit residues: 34.6803 Evaluate side-chains 91 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 315 SER Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 171 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 2.3742 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.048188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.038233 restraints weight = 104445.488| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.90 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 14646 Z= 0.195 Angle : 0.893 59.200 19751 Z= 0.510 Chirality : 0.044 0.802 2135 Planarity : 0.005 0.124 2520 Dihedral : 4.718 53.375 1899 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.68 % Allowed : 24.69 % Favored : 73.63 % Cbeta Deviations : 0.12 % 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: 0.26 (0.21), residues: 1720 helix: 1.70 (0.19), residues: 819 sheet: -1.56 (0.54), residues: 91 loop : -1.27 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 966 HIS 0.004 0.001 HIS B1252 PHE 0.035 0.001 PHE B 977 TYR 0.032 0.001 TYR F 373 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 620) hydrogen bonds : angle 4.15797 ( 1803) covalent geometry : bond 0.00426 (14646) covalent geometry : angle 0.89255 (19751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5576.42 seconds wall clock time: 99 minutes 54.93 seconds (5994.93 seconds total)