Starting phenix.real_space_refine on Sat Oct 11 11:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc7_37096/10_2025/8kc7_37096.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc7_37096/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kc7_37096/10_2025/8kc7_37096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc7_37096/10_2025/8kc7_37096.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kc7_37096/10_2025/8kc7_37096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc7_37096/10_2025/8kc7_37096.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 607.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 2.19 Time building geometry restraints manager: 1.44 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: 2.920 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- 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 : 9.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG B1009 TYR 0.020 0.001 TYR D 299 PHE 0.014 0.001 PHE G 336 TRP 0.030 0.001 TRP B 966 HIS 0.003 0.001 HIS B1252 Details of bonding type rmsd covalent geometry : bond 0.00277 (14646) covalent geometry : angle 0.69563 (19751) hydrogen bonds : bond 0.15407 ( 620) hydrogen bonds : angle 5.85265 ( 1803) *********************** 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 : 0.511 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: 0.1307 time to fit residues: 19.0199 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 : 0.494 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.1524 ------------------------------------------------------------------------------- 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 = 0.048442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.038483 restraints weight = 104836.586| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.86 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14646 Z= 0.251 Angle : 0.649 10.708 19751 Z= 0.334 Chirality : 0.042 0.157 2135 Planarity : 0.004 0.054 2520 Dihedral : 5.016 55.398 1900 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.87 % Allowed : 22.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1720 helix: 1.13 (0.18), residues: 814 sheet: -1.04 (0.52), residues: 96 loop : -1.63 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 38 TYR 0.020 0.002 TYR A 145 PHE 0.032 0.002 PHE B 977 TRP 0.016 0.002 TRP B 966 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00531 (14646) covalent geometry : angle 0.64923 (19751) hydrogen bonds : bond 0.04231 ( 620) hydrogen bonds : angle 4.59107 ( 1803) *********************** 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 100 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8216 (m) cc_final: 0.7999 (p) REVERT: A 204 MET cc_start: 0.8288 (ptt) cc_final: 0.8075 (ptt) REVERT: A 306 MET cc_start: 0.9092 (ttt) cc_final: 0.8803 (ttm) REVERT: B 844 ASN cc_start: 0.9680 (m-40) cc_final: 0.9171 (p0) REVERT: B 960 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8194 (m) REVERT: B 970 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.4786 (tptt) REVERT: E 438 MET cc_start: 0.8831 (ppp) cc_final: 0.7984 (ppp) REVERT: G 560 MET cc_start: 0.8292 (mpp) cc_final: 0.8089 (mpp) outliers start: 30 outliers final: 17 residues processed: 94 average time/residue: 0.1116 time to fit residues: 16.7630 Evaluate side-chains 84 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 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 1257 MET 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 41 SER 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 151 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B1165 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN E 325 ASN E 541 GLN F 275 GLN F 317 GLN G 329 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.046958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.036959 restraints weight = 105943.086| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.80 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14646 Z= 0.291 Angle : 0.697 8.636 19751 Z= 0.358 Chirality : 0.043 0.156 2135 Planarity : 0.005 0.053 2520 Dihedral : 5.255 55.884 1899 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.23 % Allowed : 23.01 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.21), residues: 1720 helix: 1.13 (0.18), residues: 818 sheet: -1.45 (0.54), residues: 92 loop : -1.50 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 50 TYR 0.024 0.002 TYR A 3 PHE 0.037 0.002 PHE B 977 TRP 0.013 0.002 TRP B1223 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00625 (14646) covalent geometry : angle 0.69744 (19751) hydrogen bonds : bond 0.04386 ( 620) hydrogen bonds : angle 4.67364 ( 1803) *********************** 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 117 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 65 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.9324 (ttt) cc_final: 0.9079 (ttm) REVERT: B 848 ASN cc_start: 0.9702 (OUTLIER) cc_final: 0.9170 (p0) REVERT: B 970 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.4962 (tptt) REVERT: B 977 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7458 (t80) REVERT: D 296 MET cc_start: 0.8761 (pmm) cc_final: 0.8474 (pmm) REVERT: E 438 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7957 (ppp) REVERT: F 275 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: G 316 MET cc_start: 0.8342 (pmm) cc_final: 0.8076 (pmm) outliers start: 52 outliers final: 26 residues processed: 110 average time/residue: 0.1007 time to fit residues: 17.9699 Evaluate side-chains 94 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 258 ILE 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 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 977 PHE Chi-restraints excluded: chain B residue 1028 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 231 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 335 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 48 LEU 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 275 GLN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 574 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 129 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** D 358 GLN F 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.048108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.038076 restraints weight = 104148.916| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.88 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14646 Z= 0.143 Angle : 0.572 12.296 19751 Z= 0.291 Chirality : 0.040 0.159 2135 Planarity : 0.004 0.054 2520 Dihedral : 5.049 55.234 1899 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.36 % Allowed : 24.13 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1720 helix: 1.39 (0.18), residues: 817 sheet: -1.46 (0.54), residues: 92 loop : -1.39 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 51 TYR 0.017 0.001 TYR A 145 PHE 0.029 0.001 PHE B 977 TRP 0.014 0.001 TRP B 966 HIS 0.004 0.001 HIS B1252 Details of bonding type rmsd covalent geometry : bond 0.00312 (14646) covalent geometry : angle 0.57194 (19751) hydrogen bonds : bond 0.03752 ( 620) hydrogen bonds : angle 4.34969 ( 1803) *********************** 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 : 0.555 Fit side-chains revert: symmetry clash REVERT: B 848 ASN cc_start: 0.9717 (OUTLIER) cc_final: 0.9223 (p0) REVERT: B 970 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.5066 (tptt) REVERT: E 438 MET cc_start: 0.8928 (ppp) cc_final: 0.8104 (ppp) REVERT: F 255 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: F 256 MET cc_start: 0.7662 (mpp) cc_final: 0.7256 (ptp) REVERT: G 316 MET cc_start: 0.8390 (pmm) cc_final: 0.8170 (pmm) outliers start: 38 outliers final: 20 residues processed: 102 average time/residue: 0.1116 time to fit residues: 18.1002 Evaluate side-chains 88 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 691 LEU 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 1018 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1258 THR Chi-restraints excluded: chain B residue 1283 GLN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 358 GLN 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 353 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 317 GLN 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 57 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 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 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.046908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.036925 restraints weight = 106056.763| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.83 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14646 Z= 0.276 Angle : 0.665 11.164 19751 Z= 0.338 Chirality : 0.042 0.183 2135 Planarity : 0.004 0.050 2520 Dihedral : 5.190 56.052 1899 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.92 % Allowed : 23.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.21), residues: 1720 helix: 1.30 (0.18), residues: 817 sheet: -1.15 (0.58), residues: 81 loop : -1.43 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 35 TYR 0.024 0.002 TYR A 3 PHE 0.032 0.002 PHE B 977 TRP 0.010 0.001 TRP E 492 HIS 0.005 0.001 HIS B1252 Details of bonding type rmsd covalent geometry : bond 0.00594 (14646) covalent geometry : angle 0.66457 (19751) hydrogen bonds : bond 0.04080 ( 620) hydrogen bonds : angle 4.50855 ( 1803) *********************** 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 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 62 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: B 848 ASN cc_start: 0.9737 (OUTLIER) cc_final: 0.9248 (p0) REVERT: B 970 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.5029 (tptt) REVERT: B 1303 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7405 (mm) REVERT: D 296 MET cc_start: 0.8755 (pmm) cc_final: 0.8451 (pmm) REVERT: E 438 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7892 (ppp) REVERT: F 255 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: G 316 MET cc_start: 0.8425 (pmm) cc_final: 0.8186 (pmm) outliers start: 63 outliers final: 36 residues processed: 118 average time/residue: 0.0940 time to fit residues: 17.7749 Evaluate side-chains 103 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 307 VAL 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 912 TRP Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 970 LYS Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1180 PHE 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 B residue 1283 GLN Chi-restraints excluded: chain B residue 1295 SER Chi-restraints excluded: chain B residue 1303 ILE 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 D residue 257 VAL Chi-restraints excluded: chain D residue 388 VAL 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 E residue 470 SER Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 287 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 0.0040 chunk 136 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 138 optimal weight: 0.0060 overall best weight: 0.6810 ------------------------------------------------------------------------------- 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** E 268 GLN F 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.048660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.038803 restraints weight = 103840.178| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.81 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14646 Z= 0.109 Angle : 0.559 10.658 19751 Z= 0.283 Chirality : 0.039 0.164 2135 Planarity : 0.004 0.054 2520 Dihedral : 4.950 54.290 1899 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.36 % Allowed : 24.88 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1720 helix: 1.55 (0.19), residues: 826 sheet: -1.80 (0.50), residues: 103 loop : -1.34 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 496 TYR 0.018 0.001 TYR D 299 PHE 0.026 0.001 PHE B 977 TRP 0.014 0.001 TRP B 966 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00233 (14646) covalent geometry : angle 0.55917 (19751) hydrogen bonds : bond 0.03475 ( 620) hydrogen bonds : angle 4.19107 ( 1803) *********************** 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 106 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: B 970 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.5139 (tptt) REVERT: B 1303 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7450 (mm) REVERT: E 438 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8082 (ppp) REVERT: F 255 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: F 256 MET cc_start: 0.8054 (ptp) cc_final: 0.7474 (ptp) outliers start: 38 outliers final: 22 residues processed: 97 average time/residue: 0.1048 time to fit residues: 16.2978 Evaluate side-chains 92 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 666 VAL 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 1192 SER Chi-restraints excluded: chain B residue 1303 ILE 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 291 ILE Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 255 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 9 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** F 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.048485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.038596 restraints weight = 103713.050| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.83 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14646 Z= 0.121 Angle : 0.568 9.943 19751 Z= 0.284 Chirality : 0.040 0.159 2135 Planarity : 0.004 0.051 2520 Dihedral : 4.774 53.077 1899 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.30 % Allowed : 25.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1720 helix: 1.63 (0.19), residues: 826 sheet: -1.80 (0.50), residues: 101 loop : -1.29 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.018 0.001 TYR D 299 PHE 0.030 0.001 PHE B 977 TRP 0.010 0.001 TRP B 966 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00265 (14646) covalent geometry : angle 0.56757 (19751) hydrogen bonds : bond 0.03417 ( 620) hydrogen bonds : angle 4.14797 ( 1803) *********************** 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 105 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: B 970 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.5220 (tptt) REVERT: B 1303 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7442 (mm) REVERT: E 438 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7871 (ppp) REVERT: F 255 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: F 256 MET cc_start: 0.8032 (ptp) cc_final: 0.7440 (ptp) REVERT: F 296 MET cc_start: 0.8861 (pmm) cc_final: 0.8613 (pmm) outliers start: 37 outliers final: 24 residues processed: 99 average time/residue: 0.1128 time to fit residues: 17.7084 Evaluate side-chains 94 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 754 SER 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 1207 VAL Chi-restraints excluded: chain B residue 1295 SER Chi-restraints excluded: chain B residue 1303 ILE 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 41 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 574 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 125 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 153 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.049110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.039229 restraints weight = 102651.781| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.82 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14646 Z= 0.103 Angle : 0.562 11.059 19751 Z= 0.279 Chirality : 0.039 0.156 2135 Planarity : 0.003 0.053 2520 Dihedral : 4.682 51.519 1899 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.99 % Allowed : 25.87 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1720 helix: 1.72 (0.19), residues: 831 sheet: -1.83 (0.50), residues: 99 loop : -1.29 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.018 0.001 TYR D 299 PHE 0.026 0.001 PHE B 977 TRP 0.010 0.001 TRP B 966 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00221 (14646) covalent geometry : angle 0.56187 (19751) hydrogen bonds : bond 0.03265 ( 620) hydrogen bonds : angle 4.06801 ( 1803) *********************** 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 100 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8605 (ptm) cc_final: 0.8385 (ttp) REVERT: B 970 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.5354 (tptt) REVERT: B 1303 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7546 (mm) REVERT: E 438 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7908 (ppp) REVERT: F 255 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: F 296 MET cc_start: 0.8866 (pmm) cc_final: 0.8639 (pmm) REVERT: G 560 MET cc_start: 0.8369 (mpp) cc_final: 0.8043 (mpp) outliers start: 32 outliers final: 23 residues processed: 96 average time/residue: 0.1169 time to fit residues: 17.5242 Evaluate side-chains 94 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 934 THR 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 1287 ARG Chi-restraints excluded: chain B residue 1295 SER Chi-restraints excluded: chain B residue 1303 ILE 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 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 390 SER Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** F 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.048809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.038951 restraints weight = 104036.106| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.81 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14646 Z= 0.114 Angle : 0.560 11.680 19751 Z= 0.278 Chirality : 0.039 0.154 2135 Planarity : 0.004 0.051 2520 Dihedral : 4.568 50.410 1899 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.87 % Allowed : 26.06 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1720 helix: 1.75 (0.19), residues: 830 sheet: -1.61 (0.50), residues: 101 loop : -1.27 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 381 TYR 0.017 0.001 TYR D 299 PHE 0.028 0.001 PHE B 977 TRP 0.008 0.001 TRP B 966 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00249 (14646) covalent geometry : angle 0.56006 (19751) hydrogen bonds : bond 0.03275 ( 620) hydrogen bonds : angle 4.03836 ( 1803) *********************** 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 96 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1303 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7526 (mm) REVERT: E 438 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.7765 (ppp) REVERT: F 255 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: F 256 MET cc_start: 0.8092 (ptp) cc_final: 0.7443 (ptp) REVERT: F 296 MET cc_start: 0.8877 (pmm) cc_final: 0.8674 (pmm) REVERT: G 560 MET cc_start: 0.8369 (mpp) cc_final: 0.8112 (mpp) outliers start: 30 outliers final: 25 residues processed: 92 average time/residue: 0.1116 time to fit residues: 16.4064 Evaluate side-chains 94 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1192 SER Chi-restraints excluded: chain B residue 1287 ARG Chi-restraints excluded: chain B residue 1295 SER Chi-restraints excluded: chain B residue 1303 ILE 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 41 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 148 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.048859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.039043 restraints weight = 103937.280| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.86 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 14646 Z= 0.120 Angle : 0.782 59.193 19751 Z= 0.433 Chirality : 0.039 0.362 2135 Planarity : 0.003 0.052 2520 Dihedral : 4.391 50.438 1895 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 1.87 % Allowed : 26.12 % Favored : 72.01 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1720 helix: 1.75 (0.19), residues: 830 sheet: -1.59 (0.51), residues: 101 loop : -1.28 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 381 TYR 0.017 0.001 TYR D 299 PHE 0.028 0.001 PHE B 977 TRP 0.009 0.001 TRP B 966 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00257 (14646) covalent geometry : angle 0.78220 (19751) hydrogen bonds : bond 0.03274 ( 620) hydrogen bonds : angle 4.03734 ( 1803) ********************** 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 96 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1303 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7538 (mm) REVERT: E 438 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.7774 (ppp) REVERT: F 255 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: F 256 MET cc_start: 0.8103 (ptp) cc_final: 0.7483 (ptp) REVERT: F 296 MET cc_start: 0.8893 (pmm) cc_final: 0.8688 (pmm) outliers start: 30 outliers final: 27 residues processed: 92 average time/residue: 0.1077 time to fit residues: 15.8860 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 : 0.505 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 960 THR 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 1287 ARG Chi-restraints excluded: chain B residue 1295 SER Chi-restraints excluded: chain B residue 1303 ILE 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 41 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 164 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 133 optimal weight: 8.9990 chunk 159 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.048741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.038988 restraints weight = 103604.914| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.77 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14646 Z= 0.139 Angle : 0.768 59.198 19751 Z= 0.421 Chirality : 0.040 0.348 2135 Planarity : 0.003 0.051 2520 Dihedral : 4.390 50.461 1895 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 1.93 % Allowed : 26.00 % Favored : 72.08 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.21), residues: 1720 helix: 1.74 (0.19), residues: 830 sheet: -1.59 (0.51), residues: 101 loop : -1.29 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 381 TYR 0.017 0.001 TYR D 299 PHE 0.029 0.001 PHE B 977 TRP 0.009 0.001 TRP B 966 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00295 (14646) covalent geometry : angle 0.76817 (19751) hydrogen bonds : bond 0.03280 ( 620) hydrogen bonds : angle 4.03876 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.17 seconds wall clock time: 40 minutes 0.84 seconds (2400.84 seconds total)