Starting phenix.real_space_refine on Thu Sep 18 04:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggc_51327/09_2025/9ggc_51327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggc_51327/09_2025/9ggc_51327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ggc_51327/09_2025/9ggc_51327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggc_51327/09_2025/9ggc_51327.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggc_51327/09_2025/9ggc_51327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggc_51327/09_2025/9ggc_51327.cif" } resolution = 2.39 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= 0.000 sd= 0.979 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 41 5.49 5 S 80 5.16 5 C 8747 2.51 5 N 2447 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13930 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7430 Classifications: {'peptide': 933} Link IDs: {'PTRANS': 62, 'TRANS': 870} Chain breaks: 5 Chain: "B" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2850 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 335} Chain breaks: 3 Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2842 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 334} Chain breaks: 3 Chain: "P" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.48, per 1000 atoms: 0.25 Number of scatterers: 13930 At special positions: 0 Unit cell: (103.5, 101.844, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 80 16.00 P 41 15.00 O 2614 8.00 N 2447 7.00 C 8747 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: 1.22 Conformation dependent library (CDL) restraints added in 518.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3042 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 47.7% alpha, 13.8% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.649A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.585A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.854A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.668A pdb=" N GLY A 303 " --> pdb=" O MET A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.591A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 4.057A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.635A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.556A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.794A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 871 through 878 removed outlier: 4.545A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 942 through 955 removed outlier: 3.523A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 987 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.992A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.538A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 198 removed outlier: 4.671A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.003A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.830A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.809A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.567A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.047A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.561A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.592A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.822A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.455A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 621 through 625 removed outlier: 4.327A pdb=" N PHE A 749 " --> pdb=" O TYR A 739 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.884A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.190A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.979A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.374A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 274 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.541A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.334A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4103 1.34 - 1.45: 2449 1.45 - 1.57: 7606 1.57 - 1.69: 79 1.69 - 1.81: 126 Bond restraints: 14363 Sorted by residual: bond pdb=" C6 DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 1.375 1.332 0.043 1.20e-02 6.94e+03 1.28e+01 bond pdb=" C4 DCP A1302 " pdb=" C5 DCP A1302 " ideal model delta sigma weight residual 1.426 1.385 0.041 1.20e-02 6.94e+03 1.16e+01 bond pdb=" O1A DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.477 1.504 -0.027 1.00e-02 1.00e+04 7.33e+00 bond pdb=" O1B DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.477 1.506 -0.029 1.10e-02 8.26e+03 7.08e+00 bond pdb=" C5 DCP A1302 " pdb=" C6 DCP A1302 " ideal model delta sigma weight residual 1.345 1.385 -0.040 1.80e-02 3.09e+03 4.88e+00 ... (remaining 14358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 19587 3.02 - 6.03: 40 6.03 - 9.05: 2 9.05 - 12.06: 0 12.06 - 15.08: 2 Bond angle restraints: 19631 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 124.79 15.08 1.00e+00 1.00e+00 2.27e+02 angle pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 136.83 122.39 14.44 1.00e+00 1.00e+00 2.08e+02 angle pdb=" O1G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 110.47 103.21 7.26 1.64e+00 3.70e-01 1.95e+01 angle pdb=" C2' DCP A1302 " pdb=" C1' DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 113.92 108.90 5.02 1.28e+00 6.12e-01 1.54e+01 angle pdb=" N ILE C 300 " pdb=" CA ILE C 300 " pdb=" C ILE C 300 " ideal model delta sigma weight residual 113.71 109.98 3.73 9.50e-01 1.11e+00 1.54e+01 ... (remaining 19626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 7829 17.24 - 34.48: 451 34.48 - 51.72: 137 51.72 - 68.96: 41 68.96 - 86.20: 4 Dihedral angle restraints: 8462 sinusoidal: 3746 harmonic: 4716 Sorted by residual: dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA HIS C 77 " pdb=" C HIS C 77 " pdb=" N PHE C 78 " pdb=" CA PHE C 78 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR C 243 " pdb=" C THR C 243 " pdb=" N PRO C 244 " pdb=" CA PRO C 244 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 8459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1370 0.029 - 0.058: 498 0.058 - 0.087: 120 0.087 - 0.116: 104 0.116 - 0.145: 13 Chirality restraints: 2105 Sorted by residual: chirality pdb=" C3' DCP A1302 " pdb=" C2' DCP A1302 " pdb=" C4' DCP A1302 " pdb=" O3' DCP A1302 " both_signs ideal model delta sigma weight residual False -2.68 -2.53 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE B 437 " pdb=" N ILE B 437 " pdb=" C ILE B 437 " pdb=" CB ILE B 437 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 2102 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 73 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A1200 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 483 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.019 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 83 2.56 - 3.14: 10415 3.14 - 3.73: 22542 3.73 - 4.31: 31671 4.31 - 4.90: 52236 Nonbonded interactions: 116947 Sorted by model distance: nonbonded pdb="CA CA A1301 " pdb=" O1A DCP A1302 " model vdw 1.974 2.510 nonbonded pdb="CA CA A1301 " pdb=" O2G DCP A1302 " model vdw 2.072 2.510 nonbonded pdb=" OG SER B 80 " pdb=" O GLY B 98 " model vdw 2.206 3.040 nonbonded pdb=" OG SER B 82 " pdb=" OE1 GLN B 85 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 150 " pdb=" O ARG A 288 " model vdw 2.262 3.040 ... (remaining 116942 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 137 or resid 178 through 218 or resid 230 throu \ gh 482)) selection = (chain 'C' and (resid 67 through 137 or resid 178 through 482)) } 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: 3.240 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 0.043 14363 Z= 0.130 Angle : 0.469 15.077 19631 Z= 0.283 Chirality : 0.038 0.145 2105 Planarity : 0.004 0.041 2388 Dihedral : 12.524 86.197 5420 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.35 % Allowed : 3.03 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.22 (0.21), residues: 1610 helix: 1.65 (0.20), residues: 688 sheet: 0.87 (0.33), residues: 226 loop : 0.03 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 802 TYR 0.009 0.001 TYR A1108 PHE 0.014 0.001 PHE C 403 TRP 0.010 0.001 TRP A 312 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00253 (14363) covalent geometry : angle 0.46902 (19631) hydrogen bonds : bond 0.15346 ( 672) hydrogen bonds : angle 6.44792 ( 1885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 0.467 Fit side-chains REVERT: A 289 MET cc_start: 0.8447 (ttm) cc_final: 0.8237 (ttm) REVERT: A 361 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7330 (ttm-80) REVERT: A 890 ASP cc_start: 0.7802 (t0) cc_final: 0.7271 (t0) REVERT: B 85 GLN cc_start: 0.7297 (mp10) cc_final: 0.6916 (mp10) REVERT: B 231 ILE cc_start: 0.7264 (mm) cc_final: 0.6980 (mt) REVERT: B 322 LEU cc_start: 0.8290 (mp) cc_final: 0.8011 (mt) REVERT: B 462 MET cc_start: 0.7227 (mmp) cc_final: 0.6953 (mmp) REVERT: B 465 MET cc_start: 0.7614 (mmt) cc_final: 0.7410 (mmt) REVERT: C 180 LYS cc_start: 0.4981 (tppt) cc_final: 0.4637 (tppt) REVERT: C 314 MET cc_start: 0.7432 (mtt) cc_final: 0.7096 (ttm) REVERT: C 422 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5512 (mp10) REVERT: C 449 GLU cc_start: 0.6076 (mt-10) cc_final: 0.5863 (mm-30) outliers start: 5 outliers final: 4 residues processed: 323 average time/residue: 0.6899 time to fit residues: 240.0140 Evaluate side-chains 205 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 201 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 371 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 134 ASN A 390 GLN A 468 ASN A 565 HIS B 187 HIS B 258 HIS B 305 ASN B 309 HIS B 313 HIS ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.179233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.140515 restraints weight = 13944.444| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.12 r_work: 0.3647 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14363 Z= 0.264 Angle : 0.635 6.484 19631 Z= 0.331 Chirality : 0.046 0.155 2105 Planarity : 0.006 0.066 2388 Dihedral : 13.946 73.681 2206 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 10.98 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.95 (0.20), residues: 1610 helix: 1.29 (0.19), residues: 697 sheet: 1.01 (0.33), residues: 221 loop : -0.08 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 807 TYR 0.016 0.002 TYR A 363 PHE 0.018 0.002 PHE A1129 TRP 0.014 0.002 TRP A 441 HIS 0.009 0.002 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00619 (14363) covalent geometry : angle 0.63523 (19631) hydrogen bonds : bond 0.05111 ( 672) hydrogen bonds : angle 5.37130 ( 1885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7198 (p0) REVERT: A 361 ARG cc_start: 0.6855 (ttm-80) cc_final: 0.6450 (ttm-80) REVERT: A 385 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.5461 (mp) REVERT: A 477 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 481 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 1121 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: A 1144 GLU cc_start: 0.6492 (mp0) cc_final: 0.6178 (pm20) REVERT: B 85 GLN cc_start: 0.6619 (mp10) cc_final: 0.6330 (mp10) REVERT: B 122 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5812 (mmt90) REVERT: B 231 ILE cc_start: 0.5931 (mm) cc_final: 0.5490 (mt) REVERT: C 180 LYS cc_start: 0.2889 (tppt) cc_final: 0.2431 (tppt) REVERT: C 314 MET cc_start: 0.6760 (mtt) cc_final: 0.6054 (ttm) REVERT: C 386 ASP cc_start: 0.6836 (t0) cc_final: 0.6073 (m-30) REVERT: C 421 MET cc_start: 0.5690 (tmm) cc_final: 0.5475 (tmm) REVERT: C 422 GLN cc_start: 0.6127 (mm-40) cc_final: 0.5416 (mp10) REVERT: C 427 GLN cc_start: 0.6479 (mt0) cc_final: 0.6084 (mp10) REVERT: C 449 GLU cc_start: 0.5063 (mt-10) cc_final: 0.4720 (mm-30) outliers start: 48 outliers final: 18 residues processed: 227 average time/residue: 0.6569 time to fit residues: 161.9590 Evaluate side-chains 209 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 0.0270 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** C 210 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 = 0.4313 r_free = 0.4313 target = 0.181627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135785 restraints weight = 13967.063| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.99 r_work: 0.3706 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14363 Z= 0.140 Angle : 0.511 5.661 19631 Z= 0.270 Chirality : 0.040 0.143 2105 Planarity : 0.005 0.060 2388 Dihedral : 13.786 64.541 2206 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.32 % Allowed : 12.95 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.17 (0.20), residues: 1610 helix: 1.57 (0.19), residues: 690 sheet: 0.92 (0.33), residues: 218 loop : 0.02 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 818 TYR 0.016 0.002 TYR C 193 PHE 0.015 0.001 PHE C 403 TRP 0.019 0.001 TRP B 241 HIS 0.008 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00316 (14363) covalent geometry : angle 0.51130 (19631) hydrogen bonds : bond 0.04018 ( 672) hydrogen bonds : angle 5.06279 ( 1885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7769 (m-30) cc_final: 0.7517 (m-30) REVERT: A 177 ARG cc_start: 0.5785 (ttt-90) cc_final: 0.5403 (ttp80) REVERT: A 248 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5915 (mp0) REVERT: A 361 ARG cc_start: 0.6823 (ttm-80) cc_final: 0.6387 (ttm-80) REVERT: A 481 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 1121 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: A 1144 GLU cc_start: 0.6320 (mp0) cc_final: 0.5990 (pm20) REVERT: B 85 GLN cc_start: 0.6834 (mp10) cc_final: 0.6512 (mp10) REVERT: B 231 ILE cc_start: 0.6009 (mm) cc_final: 0.5570 (mt) REVERT: B 322 LEU cc_start: 0.6646 (mp) cc_final: 0.6396 (mt) REVERT: B 421 MET cc_start: 0.8119 (ptm) cc_final: 0.7538 (tmm) REVERT: C 180 LYS cc_start: 0.2820 (tppt) cc_final: 0.2375 (tppt) REVERT: C 314 MET cc_start: 0.6707 (mtt) cc_final: 0.6023 (ttm) REVERT: C 449 GLU cc_start: 0.4986 (mt-10) cc_final: 0.4601 (mm-30) REVERT: C 469 SER cc_start: 0.8167 (t) cc_final: 0.7650 (p) outliers start: 33 outliers final: 16 residues processed: 219 average time/residue: 0.6630 time to fit residues: 157.4860 Evaluate side-chains 206 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 100 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 43 optimal weight: 0.0870 chunk 80 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** C 210 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 = 0.4320 r_free = 0.4320 target = 0.182163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.144673 restraints weight = 14035.311| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.28 r_work: 0.3683 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14363 Z= 0.130 Angle : 0.494 5.441 19631 Z= 0.261 Chirality : 0.040 0.143 2105 Planarity : 0.004 0.048 2388 Dihedral : 13.643 59.854 2206 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.67 % Allowed : 13.30 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.30 (0.20), residues: 1610 helix: 1.71 (0.20), residues: 692 sheet: 0.87 (0.33), residues: 220 loop : 0.07 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.020 0.002 TYR C 193 PHE 0.014 0.001 PHE C 403 TRP 0.022 0.001 TRP B 241 HIS 0.009 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00294 (14363) covalent geometry : angle 0.49404 (19631) hydrogen bonds : bond 0.03703 ( 672) hydrogen bonds : angle 4.88670 ( 1885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7790 (m-30) cc_final: 0.7550 (m-30) REVERT: A 177 ARG cc_start: 0.5797 (ttt-90) cc_final: 0.5437 (ttt-90) REVERT: A 248 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: A 361 ARG cc_start: 0.6883 (ttm-80) cc_final: 0.6477 (ttm-80) REVERT: A 385 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5354 (mp) REVERT: A 477 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 769 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.5727 (m-30) REVERT: A 1121 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6423 (tm-30) REVERT: A 1144 GLU cc_start: 0.6385 (mp0) cc_final: 0.6080 (pm20) REVERT: B 85 GLN cc_start: 0.6748 (mp10) cc_final: 0.6458 (mp10) REVERT: B 231 ILE cc_start: 0.6021 (mm) cc_final: 0.5568 (mt) REVERT: B 322 LEU cc_start: 0.6540 (mp) cc_final: 0.6311 (mt) REVERT: B 421 MET cc_start: 0.8208 (ptm) cc_final: 0.7219 (pp-130) REVERT: B 450 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6396 (p0) REVERT: C 180 LYS cc_start: 0.2848 (tppt) cc_final: 0.2388 (tppt) REVERT: C 258 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5644 (m170) REVERT: C 314 MET cc_start: 0.6619 (mtt) cc_final: 0.5946 (ttm) REVERT: C 400 GLN cc_start: 0.6726 (mm-40) cc_final: 0.6407 (tm-30) REVERT: C 422 GLN cc_start: 0.6344 (mm-40) cc_final: 0.5682 (mp10) REVERT: C 427 GLN cc_start: 0.6407 (mt0) cc_final: 0.5987 (mp10) REVERT: C 449 GLU cc_start: 0.4962 (mt-10) cc_final: 0.4584 (mm-30) REVERT: C 465 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6302 (mmm) REVERT: C 466 MET cc_start: 0.7997 (ttm) cc_final: 0.7595 (ttm) REVERT: C 469 SER cc_start: 0.8227 (t) cc_final: 0.7729 (p) outliers start: 38 outliers final: 16 residues processed: 210 average time/residue: 0.6505 time to fit residues: 148.7306 Evaluate side-chains 196 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 GLN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS C 96 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.179647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.141799 restraints weight = 14042.650| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.29 r_work: 0.3646 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14363 Z= 0.183 Angle : 0.546 6.087 19631 Z= 0.286 Chirality : 0.041 0.147 2105 Planarity : 0.005 0.046 2388 Dihedral : 13.772 62.194 2205 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.96 % Allowed : 13.44 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.16 (0.20), residues: 1610 helix: 1.57 (0.19), residues: 692 sheet: 0.79 (0.33), residues: 215 loop : 0.04 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 818 TYR 0.021 0.002 TYR C 193 PHE 0.014 0.002 PHE A1129 TRP 0.019 0.001 TRP B 241 HIS 0.010 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00427 (14363) covalent geometry : angle 0.54555 (19631) hydrogen bonds : bond 0.04146 ( 672) hydrogen bonds : angle 4.99702 ( 1885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.554 Fit side-chains REVERT: A 158 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5840 (mp) REVERT: A 177 ARG cc_start: 0.5827 (ttt-90) cc_final: 0.5457 (ttt-90) REVERT: A 248 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: A 361 ARG cc_start: 0.6908 (ttm-80) cc_final: 0.6497 (ttm-80) REVERT: A 371 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7762 (ptpp) REVERT: A 385 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5496 (mp) REVERT: A 481 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 1121 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: A 1164 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6771 (t80) REVERT: B 231 ILE cc_start: 0.6023 (mm) cc_final: 0.5555 (mt) REVERT: B 322 LEU cc_start: 0.6583 (mp) cc_final: 0.6352 (mt) REVERT: B 421 MET cc_start: 0.8177 (ptm) cc_final: 0.7172 (pp-130) REVERT: B 450 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6443 (p0) REVERT: C 180 LYS cc_start: 0.2920 (tppt) cc_final: 0.2470 (tppt) REVERT: C 258 HIS cc_start: 0.6072 (OUTLIER) cc_final: 0.5712 (m170) REVERT: C 314 MET cc_start: 0.6705 (mtt) cc_final: 0.5994 (ttm) REVERT: C 400 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6538 (tm-30) REVERT: C 422 GLN cc_start: 0.6275 (mm-40) cc_final: 0.5611 (mp10) REVERT: C 427 GLN cc_start: 0.6458 (mt0) cc_final: 0.6053 (mp10) REVERT: C 449 GLU cc_start: 0.4998 (mt-10) cc_final: 0.4618 (mm-30) REVERT: C 469 SER cc_start: 0.8227 (t) cc_final: 0.7721 (p) outliers start: 42 outliers final: 23 residues processed: 210 average time/residue: 0.6619 time to fit residues: 151.4368 Evaluate side-chains 203 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.180606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.134705 restraints weight = 14028.567| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.00 r_work: 0.3690 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14363 Z= 0.149 Angle : 0.514 6.910 19631 Z= 0.270 Chirality : 0.040 0.144 2105 Planarity : 0.004 0.045 2388 Dihedral : 13.689 59.495 2205 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.74 % Allowed : 13.86 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.28 (0.20), residues: 1610 helix: 1.65 (0.19), residues: 692 sheet: 0.92 (0.32), residues: 221 loop : 0.10 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.019 0.002 TYR C 193 PHE 0.013 0.001 PHE C 403 TRP 0.023 0.001 TRP B 241 HIS 0.009 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00343 (14363) covalent geometry : angle 0.51378 (19631) hydrogen bonds : bond 0.03810 ( 672) hydrogen bonds : angle 4.91077 ( 1885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.536 Fit side-chains REVERT: A 75 ASP cc_start: 0.7746 (m-30) cc_final: 0.7520 (m-30) REVERT: A 177 ARG cc_start: 0.5769 (ttt-90) cc_final: 0.5394 (ttt-90) REVERT: A 226 GLN cc_start: 0.6991 (mt0) cc_final: 0.6472 (pt0) REVERT: A 248 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5822 (mp0) REVERT: A 361 ARG cc_start: 0.6815 (ttm-80) cc_final: 0.6396 (ttm-80) REVERT: A 371 LYS cc_start: 0.8378 (ptmt) cc_final: 0.7592 (ptpp) REVERT: A 385 ILE cc_start: 0.6135 (OUTLIER) cc_final: 0.5334 (mp) REVERT: A 481 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 581 ASP cc_start: 0.6903 (m-30) cc_final: 0.6641 (p0) REVERT: A 1192 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 71 GLU cc_start: 0.6211 (tp30) cc_final: 0.5896 (tp30) REVERT: B 231 ILE cc_start: 0.6085 (mm) cc_final: 0.5622 (mt) REVERT: B 421 MET cc_start: 0.8170 (ptm) cc_final: 0.7164 (pp-130) REVERT: B 450 ASN cc_start: 0.6676 (OUTLIER) cc_final: 0.6472 (p0) REVERT: C 180 LYS cc_start: 0.2828 (tppt) cc_final: 0.2603 (tppt) REVERT: C 258 HIS cc_start: 0.6014 (OUTLIER) cc_final: 0.5646 (m170) REVERT: C 314 MET cc_start: 0.6660 (mtt) cc_final: 0.5957 (ttm) REVERT: C 400 GLN cc_start: 0.6789 (mm-40) cc_final: 0.6467 (tm-30) REVERT: C 422 GLN cc_start: 0.6287 (mm-40) cc_final: 0.5645 (mp10) REVERT: C 427 GLN cc_start: 0.6415 (mt0) cc_final: 0.5996 (mp10) REVERT: C 449 GLU cc_start: 0.4939 (mt-10) cc_final: 0.4570 (mm-30) REVERT: C 466 MET cc_start: 0.7948 (ttm) cc_final: 0.7630 (ttm) REVERT: C 469 SER cc_start: 0.8177 (t) cc_final: 0.7673 (p) outliers start: 39 outliers final: 19 residues processed: 209 average time/residue: 0.6537 time to fit residues: 149.2180 Evaluate side-chains 200 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 88 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 0.0030 chunk 40 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS C 210 GLN C 250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.181944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.136445 restraints weight = 13983.112| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.99 r_work: 0.3709 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14363 Z= 0.123 Angle : 0.492 7.167 19631 Z= 0.259 Chirality : 0.039 0.142 2105 Planarity : 0.004 0.045 2388 Dihedral : 13.573 59.495 2205 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.53 % Allowed : 14.07 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.41 (0.20), residues: 1610 helix: 1.77 (0.20), residues: 692 sheet: 1.04 (0.33), residues: 217 loop : 0.14 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.019 0.002 TYR A 479 PHE 0.014 0.001 PHE C 403 TRP 0.027 0.001 TRP B 241 HIS 0.010 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00277 (14363) covalent geometry : angle 0.49234 (19631) hydrogen bonds : bond 0.03569 ( 672) hydrogen bonds : angle 4.80771 ( 1885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.555 Fit side-chains REVERT: A 75 ASP cc_start: 0.7742 (m-30) cc_final: 0.7521 (m-30) REVERT: A 158 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5718 (mp) REVERT: A 177 ARG cc_start: 0.5750 (ttt-90) cc_final: 0.5377 (ttt-90) REVERT: A 226 GLN cc_start: 0.6958 (mt0) cc_final: 0.6420 (pt0) REVERT: A 248 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5694 (mp0) REVERT: A 361 ARG cc_start: 0.6799 (ttm-80) cc_final: 0.6386 (ttm-80) REVERT: A 371 LYS cc_start: 0.8360 (ptmt) cc_final: 0.7585 (ptpp) REVERT: A 385 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5266 (mp) REVERT: A 1121 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: B 71 GLU cc_start: 0.6219 (tp30) cc_final: 0.5921 (tp30) REVERT: B 322 LEU cc_start: 0.6572 (mp) cc_final: 0.6338 (mt) REVERT: B 421 MET cc_start: 0.8205 (ptm) cc_final: 0.7199 (pp-130) REVERT: C 71 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6090 (tt0) REVERT: C 180 LYS cc_start: 0.2838 (tppt) cc_final: 0.2630 (tppt) REVERT: C 254 PHE cc_start: 0.7065 (t80) cc_final: 0.6714 (t80) REVERT: C 258 HIS cc_start: 0.6018 (OUTLIER) cc_final: 0.5726 (m170) REVERT: C 314 MET cc_start: 0.6661 (mtt) cc_final: 0.5965 (ttm) REVERT: C 400 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6464 (tm-30) REVERT: C 422 GLN cc_start: 0.6250 (mm-40) cc_final: 0.5606 (mp10) REVERT: C 427 GLN cc_start: 0.6457 (mt0) cc_final: 0.6045 (mp10) REVERT: C 449 GLU cc_start: 0.4916 (mt-10) cc_final: 0.4559 (mm-30) REVERT: C 466 MET cc_start: 0.7965 (ttm) cc_final: 0.7573 (ttm) REVERT: C 469 SER cc_start: 0.8136 (t) cc_final: 0.7659 (p) outliers start: 36 outliers final: 22 residues processed: 205 average time/residue: 0.7093 time to fit residues: 157.8182 Evaluate side-chains 202 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 148 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS B 313 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.177185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130815 restraints weight = 13913.884| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.97 r_work: 0.3643 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14363 Z= 0.270 Angle : 0.635 7.902 19631 Z= 0.328 Chirality : 0.045 0.167 2105 Planarity : 0.005 0.051 2388 Dihedral : 13.913 68.639 2205 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.96 % Allowed : 14.29 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.90 (0.20), residues: 1610 helix: 1.31 (0.19), residues: 691 sheet: 0.55 (0.32), residues: 229 loop : -0.02 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 807 TYR 0.026 0.003 TYR A 479 PHE 0.018 0.002 PHE A1129 TRP 0.027 0.002 TRP B 241 HIS 0.009 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00641 (14363) covalent geometry : angle 0.63454 (19631) hydrogen bonds : bond 0.04715 ( 672) hydrogen bonds : angle 5.16787 ( 1885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.681 Fit side-chains REVERT: A 158 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5889 (mp) REVERT: A 177 ARG cc_start: 0.5799 (ttt-90) cc_final: 0.5360 (ttt-90) REVERT: A 226 GLN cc_start: 0.7031 (mt0) cc_final: 0.6492 (pt0) REVERT: A 361 ARG cc_start: 0.6875 (ttm-80) cc_final: 0.6495 (ttm-80) REVERT: A 371 LYS cc_start: 0.8362 (ptmt) cc_final: 0.7631 (ptpp) REVERT: A 385 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5549 (mp) REVERT: A 581 ASP cc_start: 0.6987 (m-30) cc_final: 0.6651 (p0) REVERT: A 833 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8040 (tp30) REVERT: A 1121 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6457 (tm-30) REVERT: B 71 GLU cc_start: 0.6294 (tp30) cc_final: 0.5998 (tp30) REVERT: B 180 LYS cc_start: 0.5903 (tptt) cc_final: 0.5660 (tptt) REVERT: B 185 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5394 (mt) REVERT: B 231 ILE cc_start: 0.6343 (mm) cc_final: 0.5982 (mt) REVERT: B 394 GLU cc_start: 0.7563 (tp30) cc_final: 0.7086 (mp0) REVERT: B 421 MET cc_start: 0.8181 (ptm) cc_final: 0.7158 (pp-130) REVERT: C 71 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6100 (tt0) REVERT: C 180 LYS cc_start: 0.2817 (tppt) cc_final: 0.2573 (tppt) REVERT: C 299 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6228 (tp) REVERT: C 400 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6402 (tm-30) REVERT: C 422 GLN cc_start: 0.6261 (mm-40) cc_final: 0.5598 (mp10) REVERT: C 427 GLN cc_start: 0.6492 (mt0) cc_final: 0.6041 (mp10) REVERT: C 449 GLU cc_start: 0.5008 (mt-10) cc_final: 0.4631 (mm-30) REVERT: C 465 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6237 (mmm) REVERT: C 466 MET cc_start: 0.8047 (ttm) cc_final: 0.7609 (ttm) REVERT: C 469 SER cc_start: 0.8164 (t) cc_final: 0.7652 (p) outliers start: 42 outliers final: 28 residues processed: 214 average time/residue: 0.6556 time to fit residues: 153.2267 Evaluate side-chains 210 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.179731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133914 restraints weight = 14124.626| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.99 r_work: 0.3679 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14363 Z= 0.155 Angle : 0.539 8.297 19631 Z= 0.282 Chirality : 0.041 0.142 2105 Planarity : 0.004 0.046 2388 Dihedral : 13.764 59.428 2205 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.53 % Allowed : 14.99 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.15 (0.20), residues: 1610 helix: 1.53 (0.19), residues: 691 sheet: 0.77 (0.32), residues: 234 loop : 0.08 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.023 0.002 TYR A 479 PHE 0.014 0.001 PHE C 403 TRP 0.034 0.002 TRP B 241 HIS 0.005 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00358 (14363) covalent geometry : angle 0.53856 (19631) hydrogen bonds : bond 0.03875 ( 672) hydrogen bonds : angle 4.96562 ( 1885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.557 Fit side-chains REVERT: A 158 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5842 (mp) REVERT: A 177 ARG cc_start: 0.5813 (ttt-90) cc_final: 0.5545 (ttt180) REVERT: A 226 GLN cc_start: 0.6912 (mt0) cc_final: 0.6449 (pt0) REVERT: A 361 ARG cc_start: 0.6846 (ttm-80) cc_final: 0.6412 (ttm-80) REVERT: A 371 LYS cc_start: 0.8369 (ptmt) cc_final: 0.7612 (ptpp) REVERT: A 385 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5451 (mp) REVERT: A 581 ASP cc_start: 0.6934 (m-30) cc_final: 0.6667 (p0) REVERT: A 833 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8066 (tp30) REVERT: A 1121 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: B 71 GLU cc_start: 0.6295 (tp30) cc_final: 0.5994 (tp30) REVERT: B 231 ILE cc_start: 0.6270 (mm) cc_final: 0.5888 (mt) REVERT: B 421 MET cc_start: 0.8202 (ptm) cc_final: 0.7176 (pp-130) REVERT: C 71 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6082 (tt0) REVERT: C 180 LYS cc_start: 0.2775 (tppt) cc_final: 0.2398 (tppt) REVERT: C 400 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6488 (tm-30) REVERT: C 422 GLN cc_start: 0.6238 (mm-40) cc_final: 0.5585 (mp10) REVERT: C 427 GLN cc_start: 0.6484 (mt0) cc_final: 0.6056 (mp10) REVERT: C 449 GLU cc_start: 0.4939 (mt-10) cc_final: 0.4577 (mm-30) REVERT: C 466 MET cc_start: 0.8001 (ttm) cc_final: 0.7604 (ttm) REVERT: C 469 SER cc_start: 0.8134 (t) cc_final: 0.7656 (p) outliers start: 36 outliers final: 24 residues processed: 204 average time/residue: 0.6050 time to fit residues: 135.0137 Evaluate side-chains 203 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 114 optimal weight: 0.6980 chunk 142 optimal weight: 0.0770 chunk 144 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS C 85 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.180571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134944 restraints weight = 14024.018| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.98 r_work: 0.3692 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14363 Z= 0.140 Angle : 0.526 8.393 19631 Z= 0.275 Chirality : 0.040 0.143 2105 Planarity : 0.004 0.046 2388 Dihedral : 13.619 59.325 2204 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.18 % Allowed : 15.20 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.26 (0.20), residues: 1610 helix: 1.66 (0.20), residues: 693 sheet: 0.79 (0.32), residues: 236 loop : 0.08 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.023 0.002 TYR A 479 PHE 0.015 0.001 PHE C 403 TRP 0.038 0.001 TRP B 241 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00322 (14363) covalent geometry : angle 0.52636 (19631) hydrogen bonds : bond 0.03736 ( 672) hydrogen bonds : angle 4.86928 ( 1885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.560 Fit side-chains REVERT: A 75 ASP cc_start: 0.7787 (m-30) cc_final: 0.7577 (m-30) REVERT: A 158 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5715 (mp) REVERT: A 177 ARG cc_start: 0.5762 (ttt-90) cc_final: 0.5499 (ttt180) REVERT: A 226 GLN cc_start: 0.6777 (mt0) cc_final: 0.6332 (pt0) REVERT: A 361 ARG cc_start: 0.6818 (ttm-80) cc_final: 0.6389 (ttm-80) REVERT: A 371 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7829 (ptpp) REVERT: A 385 ILE cc_start: 0.6202 (OUTLIER) cc_final: 0.5423 (mp) REVERT: A 1121 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: B 71 GLU cc_start: 0.6222 (tp30) cc_final: 0.5914 (tp30) REVERT: B 394 GLU cc_start: 0.7535 (tp30) cc_final: 0.7055 (mp0) REVERT: B 421 MET cc_start: 0.8177 (ptm) cc_final: 0.7162 (pp-130) REVERT: C 71 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6095 (tt0) REVERT: C 180 LYS cc_start: 0.2749 (tppt) cc_final: 0.2378 (tppt) REVERT: C 400 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6476 (tm-30) REVERT: C 422 GLN cc_start: 0.6244 (mm-40) cc_final: 0.5167 (mt0) REVERT: C 427 GLN cc_start: 0.6498 (mt0) cc_final: 0.6047 (mp10) REVERT: C 449 GLU cc_start: 0.4895 (mt-10) cc_final: 0.4537 (mm-30) REVERT: C 466 MET cc_start: 0.8015 (ttm) cc_final: 0.7535 (ttm) REVERT: C 469 SER cc_start: 0.8129 (t) cc_final: 0.7662 (p) outliers start: 31 outliers final: 22 residues processed: 195 average time/residue: 0.6028 time to fit residues: 128.5312 Evaluate side-chains 196 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9990 chunk 112 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 0.0050 chunk 42 optimal weight: 0.3980 chunk 163 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.183303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138391 restraints weight = 14033.946| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.99 r_work: 0.3730 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14363 Z= 0.111 Angle : 0.492 8.332 19631 Z= 0.259 Chirality : 0.039 0.149 2105 Planarity : 0.004 0.046 2388 Dihedral : 13.438 59.749 2204 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.90 % Allowed : 15.69 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 1.43 (0.21), residues: 1610 helix: 1.78 (0.20), residues: 701 sheet: 0.81 (0.32), residues: 238 loop : 0.20 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 927 TYR 0.019 0.001 TYR A 479 PHE 0.016 0.001 PHE C 403 TRP 0.042 0.001 TRP B 241 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00250 (14363) covalent geometry : angle 0.49239 (19631) hydrogen bonds : bond 0.03353 ( 672) hydrogen bonds : angle 4.70310 ( 1885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6910.26 seconds wall clock time: 118 minutes 1.41 seconds (7081.41 seconds total)