Starting phenix.real_space_refine on Thu Jun 12 11:20:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggc_51327/06_2025/9ggc_51327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggc_51327/06_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_51327/06_2025/9ggc_51327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggc_51327/06_2025/9ggc_51327.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggc_51327/06_2025/9ggc_51327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggc_51327/06_2025/9ggc_51327.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.08, per 1000 atoms: 0.65 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: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.27 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: 5.80 Time building geometry restraints manager: 4.54 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: 1.830 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.550 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (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 TRP 0.010 0.001 TRP A 312 HIS 0.004 0.001 HIS B 77 PHE 0.014 0.001 PHE C 403 TYR 0.009 0.001 TYR A1108 ARG 0.003 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.15346 ( 672) hydrogen bonds : angle 6.44792 ( 1885) covalent geometry : bond 0.00253 (14363) covalent geometry : angle 0.46902 (19631) *********************** 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 : 1.581 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: 0.7335 (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: 1.5125 time to fit residues: 527.4281 Evaluate side-chains 206 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 140 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 390 GLN A 468 ASN B 187 HIS B 258 HIS B 305 ASN B 309 HIS B 313 HIS B 375 HIS C 258 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.182194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144322 restraints weight = 13789.367| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.10 r_work: 0.3692 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14363 Z= 0.187 Angle : 0.564 5.808 19631 Z= 0.295 Chirality : 0.042 0.149 2105 Planarity : 0.005 0.063 2388 Dihedral : 13.785 66.350 2206 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.89 % Allowed : 11.19 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1610 helix: 1.59 (0.19), residues: 690 sheet: 1.05 (0.34), residues: 216 loop : 0.03 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 241 HIS 0.010 0.001 HIS B 258 PHE 0.017 0.002 PHE A1129 TYR 0.014 0.002 TYR B 291 ARG 0.005 0.001 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 672) hydrogen bonds : angle 5.21117 ( 1885) covalent geometry : bond 0.00432 (14363) covalent geometry : angle 0.56446 (19631) *********************** 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 241 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.6896 (ttm-80) cc_final: 0.6493 (ttm-80) REVERT: A 481 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: A 1121 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: A 1144 GLU cc_start: 0.6406 (mp0) cc_final: 0.6144 (pm20) REVERT: A 1225 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: B 71 GLU cc_start: 0.6269 (tp30) cc_final: 0.5968 (tp30) REVERT: B 85 GLN cc_start: 0.6724 (mp10) cc_final: 0.6438 (mp10) REVERT: B 231 ILE cc_start: 0.5945 (mm) cc_final: 0.5499 (mt) REVERT: C 180 LYS cc_start: 0.2878 (tppt) cc_final: 0.2397 (tppt) REVERT: C 314 MET cc_start: 0.6772 (mtt) cc_final: 0.6078 (ttm) REVERT: C 386 ASP cc_start: 0.6862 (t0) cc_final: 0.6121 (m-30) REVERT: C 421 MET cc_start: 0.5733 (tmm) cc_final: 0.5516 (tmm) REVERT: C 422 GLN cc_start: 0.6164 (mm-40) cc_final: 0.5422 (mp10) REVERT: C 427 GLN cc_start: 0.6468 (mt0) cc_final: 0.6091 (mp10) REVERT: C 449 GLU cc_start: 0.4995 (mt-10) cc_final: 0.4639 (mm-30) outliers start: 41 outliers final: 20 residues processed: 223 average time/residue: 1.9872 time to fit residues: 483.3522 Evaluate side-chains 204 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 189 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 1121 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1225 GLU 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 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 B residue 395 LEU 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 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 160 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS B 258 HIS B 313 HIS B 375 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.182540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.136962 restraints weight = 13911.403| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.99 r_work: 0.3714 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1944 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= 0.139 Angle : 0.498 5.326 19631 Z= 0.263 Chirality : 0.040 0.143 2105 Planarity : 0.005 0.060 2388 Dihedral : 13.661 60.332 2206 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.74 % Allowed : 12.39 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1610 helix: 1.69 (0.20), residues: 696 sheet: 0.92 (0.33), residues: 224 loop : 0.05 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 241 HIS 0.008 0.001 HIS B 258 PHE 0.015 0.001 PHE C 403 TYR 0.020 0.002 TYR C 193 ARG 0.008 0.000 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 672) hydrogen bonds : angle 4.93553 ( 1885) covalent geometry : bond 0.00314 (14363) covalent geometry : angle 0.49808 (19631) *********************** 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 235 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7745 (m-30) cc_final: 0.7517 (m-30) REVERT: A 248 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: A 361 ARG cc_start: 0.6815 (ttm-80) cc_final: 0.6410 (ttm-80) REVERT: A 385 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5340 (mp) REVERT: A 481 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: A 1144 GLU cc_start: 0.6279 (mp0) cc_final: 0.5956 (pm20) REVERT: B 71 GLU cc_start: 0.6230 (tp30) cc_final: 0.5939 (tp30) REVERT: B 85 GLN cc_start: 0.6749 (mp10) cc_final: 0.6429 (mp10) REVERT: B 231 ILE cc_start: 0.6003 (mm) cc_final: 0.5573 (mt) REVERT: B 322 LEU cc_start: 0.6583 (mp) cc_final: 0.6334 (mt) REVERT: B 419 GLU cc_start: 0.6748 (tt0) cc_final: 0.6441 (tp30) REVERT: B 421 MET cc_start: 0.8099 (ptm) cc_final: 0.7141 (pp-130) REVERT: C 180 LYS cc_start: 0.2741 (tppt) cc_final: 0.2309 (tppt) REVERT: C 314 MET cc_start: 0.6707 (mtt) cc_final: 0.6031 (ttm) REVERT: C 386 ASP cc_start: 0.6954 (t0) cc_final: 0.6594 (t0) REVERT: C 400 GLN cc_start: 0.6629 (mm-40) cc_final: 0.6375 (tm-30) REVERT: C 421 MET cc_start: 0.5809 (tmm) cc_final: 0.5607 (tmm) REVERT: C 422 GLN cc_start: 0.6329 (mm-40) cc_final: 0.5691 (mp10) REVERT: C 449 GLU cc_start: 0.4906 (mt-10) cc_final: 0.4526 (mm-30) REVERT: C 469 SER cc_start: 0.8170 (t) cc_final: 0.7654 (p) outliers start: 39 outliers final: 17 residues processed: 222 average time/residue: 1.9420 time to fit residues: 470.2680 Evaluate side-chains 198 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 481 GLU 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 1137 VAL Chi-restraints excluded: chain A residue 1141 VAL 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 371 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 243 THR 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 134 optimal weight: 8.9990 chunk 149 optimal weight: 40.0000 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.181234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143191 restraints weight = 13813.646| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.12 r_work: 0.3681 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14363 Z= 0.154 Angle : 0.512 5.550 19631 Z= 0.269 Chirality : 0.040 0.146 2105 Planarity : 0.004 0.048 2388 Dihedral : 13.677 59.866 2206 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.46 % Allowed : 13.72 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1610 helix: 1.70 (0.20), residues: 692 sheet: 0.88 (0.32), residues: 224 loop : 0.04 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 241 HIS 0.004 0.001 HIS A 971 PHE 0.013 0.001 PHE C 403 TYR 0.020 0.002 TYR C 193 ARG 0.006 0.000 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 672) hydrogen bonds : angle 4.91494 ( 1885) covalent geometry : bond 0.00357 (14363) covalent geometry : angle 0.51234 (19631) *********************** 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 226 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.494 Fit side-chains REVERT: A 75 ASP cc_start: 0.7765 (m-30) cc_final: 0.7548 (m-30) REVERT: A 226 GLN cc_start: 0.7077 (mt0) cc_final: 0.6554 (pt0) REVERT: A 248 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5851 (mp0) REVERT: A 361 ARG cc_start: 0.6824 (ttm-80) cc_final: 0.6422 (ttm-80) REVERT: A 385 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5364 (mp) REVERT: A 1121 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6412 (tm-30) REVERT: A 1144 GLU cc_start: 0.6310 (mp0) cc_final: 0.6037 (pm20) REVERT: B 71 GLU cc_start: 0.6317 (tp30) cc_final: 0.5989 (tp30) REVERT: B 85 GLN cc_start: 0.6737 (mp10) cc_final: 0.6445 (mp10) REVERT: B 231 ILE cc_start: 0.6025 (mm) cc_final: 0.5587 (mt) REVERT: B 322 LEU cc_start: 0.6573 (mp) cc_final: 0.6340 (mt) REVERT: B 394 GLU cc_start: 0.7579 (tp30) cc_final: 0.7267 (tp30) REVERT: B 419 GLU cc_start: 0.6774 (tt0) cc_final: 0.6519 (tp30) REVERT: B 421 MET cc_start: 0.8109 (ptm) cc_final: 0.7525 (tmm) REVERT: B 450 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6332 (p0) REVERT: C 180 LYS cc_start: 0.2823 (tppt) cc_final: 0.2374 (tppt) REVERT: C 258 HIS cc_start: 0.6073 (OUTLIER) cc_final: 0.5701 (m170) REVERT: C 314 MET cc_start: 0.6642 (mtt) cc_final: 0.5956 (ttm) REVERT: C 386 ASP cc_start: 0.7048 (t0) cc_final: 0.6689 (t0) REVERT: C 400 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6388 (tm-30) REVERT: C 422 GLN cc_start: 0.6356 (mm-40) cc_final: 0.5668 (mp10) REVERT: C 427 GLN cc_start: 0.6431 (mt0) cc_final: 0.5931 (mp10) REVERT: C 449 GLU cc_start: 0.4985 (mt-10) cc_final: 0.4602 (mm-30) REVERT: C 466 MET cc_start: 0.8060 (ttm) cc_final: 0.7588 (ttm) REVERT: C 469 SER cc_start: 0.8206 (t) cc_final: 0.7705 (p) outliers start: 35 outliers final: 19 residues processed: 214 average time/residue: 1.3668 time to fit residues: 318.9080 Evaluate side-chains 202 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 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 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 261 GLN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 142 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 B 313 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.179631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141720 restraints weight = 14031.484| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.28 r_work: 0.3645 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14363 Z= 0.184 Angle : 0.546 5.955 19631 Z= 0.286 Chirality : 0.042 0.147 2105 Planarity : 0.005 0.046 2388 Dihedral : 13.780 62.249 2206 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.03 % Allowed : 13.23 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1610 helix: 1.59 (0.19), residues: 692 sheet: 0.78 (0.33), residues: 224 loop : 0.02 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 241 HIS 0.005 0.001 HIS B 258 PHE 0.014 0.002 PHE A1129 TYR 0.022 0.002 TYR C 193 ARG 0.006 0.001 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 672) hydrogen bonds : angle 4.96702 ( 1885) covalent geometry : bond 0.00428 (14363) covalent geometry : angle 0.54574 (19631) *********************** 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 232 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7789 (m-30) cc_final: 0.7575 (m-30) REVERT: A 158 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5943 (mp) REVERT: A 226 GLN cc_start: 0.7130 (mt0) cc_final: 0.6580 (pt0) REVERT: A 248 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5930 (mp0) REVERT: A 361 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6525 (ttm-80) REVERT: A 371 LYS cc_start: 0.8403 (ptmt) cc_final: 0.7772 (ptpp) REVERT: A 385 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5518 (mp) REVERT: A 481 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: A 581 ASP cc_start: 0.6934 (m-30) cc_final: 0.6669 (p0) REVERT: A 1164 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6771 (t80) REVERT: B 71 GLU cc_start: 0.6356 (tp30) cc_final: 0.6058 (tp30) REVERT: B 85 GLN cc_start: 0.6810 (mp10) cc_final: 0.6424 (mp10) REVERT: B 231 ILE cc_start: 0.6131 (mm) cc_final: 0.5682 (mt) REVERT: B 322 LEU cc_start: 0.6655 (mp) cc_final: 0.6420 (mt) REVERT: B 394 GLU cc_start: 0.7790 (tp30) cc_final: 0.7557 (tp30) REVERT: B 450 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6445 (p0) REVERT: C 180 LYS cc_start: 0.2997 (tppt) cc_final: 0.2552 (tppt) REVERT: C 258 HIS cc_start: 0.6065 (OUTLIER) cc_final: 0.5638 (m170) REVERT: C 314 MET cc_start: 0.6704 (mtt) cc_final: 0.5990 (ttm) REVERT: C 386 ASP cc_start: 0.7079 (t0) cc_final: 0.6696 (t0) REVERT: C 400 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6570 (tm-30) REVERT: C 422 GLN cc_start: 0.6319 (mm-40) cc_final: 0.5629 (mp10) REVERT: C 427 GLN cc_start: 0.6553 (mt0) cc_final: 0.6119 (mp10) REVERT: C 449 GLU cc_start: 0.5022 (mt-10) cc_final: 0.4637 (mm-30) REVERT: C 469 SER cc_start: 0.8231 (t) cc_final: 0.7723 (p) outliers start: 43 outliers final: 24 residues processed: 219 average time/residue: 1.3337 time to fit residues: 319.2088 Evaluate side-chains 207 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 100 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 B 427 GLN C 96 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.180924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143388 restraints weight = 14048.937| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.31 r_work: 0.3667 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2368 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= 0.142 Angle : 0.508 6.948 19631 Z= 0.267 Chirality : 0.040 0.143 2105 Planarity : 0.004 0.045 2388 Dihedral : 13.674 59.486 2206 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1610 helix: 1.68 (0.19), residues: 692 sheet: 0.97 (0.33), residues: 226 loop : 0.10 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 241 HIS 0.006 0.001 HIS B 258 PHE 0.014 0.001 PHE C 403 TYR 0.018 0.002 TYR C 193 ARG 0.006 0.000 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 672) hydrogen bonds : angle 4.85514 ( 1885) covalent geometry : bond 0.00326 (14363) covalent geometry : angle 0.50782 (19631) *********************** 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 219 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7773 (m-30) cc_final: 0.7560 (m-30) REVERT: A 158 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5820 (mp) REVERT: A 226 GLN cc_start: 0.7112 (mt0) cc_final: 0.6500 (pt0) REVERT: A 248 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5817 (mp0) REVERT: A 361 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6483 (ttm-80) REVERT: A 371 LYS cc_start: 0.8375 (ptmt) cc_final: 0.7853 (ptpp) REVERT: A 385 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5462 (mp) REVERT: A 481 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: A 581 ASP cc_start: 0.6907 (m-30) cc_final: 0.6662 (p0) REVERT: A 1121 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: A 1164 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6754 (t80) REVERT: B 71 GLU cc_start: 0.6311 (tp30) cc_final: 0.6000 (tp30) REVERT: B 74 GLN cc_start: 0.7014 (pt0) cc_final: 0.6778 (pt0) REVERT: B 85 GLN cc_start: 0.6767 (mp10) cc_final: 0.6410 (mp10) REVERT: B 231 ILE cc_start: 0.6110 (mm) cc_final: 0.5662 (mt) REVERT: B 394 GLU cc_start: 0.7836 (tp30) cc_final: 0.7386 (tp30) REVERT: B 450 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6435 (p0) REVERT: C 180 LYS cc_start: 0.2917 (tppt) cc_final: 0.2700 (tppt) REVERT: C 258 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5708 (m170) REVERT: C 314 MET cc_start: 0.6644 (mtt) cc_final: 0.5952 (ttm) REVERT: C 449 GLU cc_start: 0.5013 (mt-10) cc_final: 0.4641 (mm-30) REVERT: C 466 MET cc_start: 0.8028 (ttm) cc_final: 0.7672 (ttm) REVERT: C 469 SER cc_start: 0.8235 (t) cc_final: 0.7745 (p) outliers start: 39 outliers final: 24 residues processed: 208 average time/residue: 1.4537 time to fit residues: 332.0479 Evaluate side-chains 216 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 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 1164 PHE 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 261 GLN 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 B residue 450 ASN 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 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 132 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS B 287 ASN B 313 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.177655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.139556 restraints weight = 14032.828| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.23 r_work: 0.3624 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14363 Z= 0.238 Angle : 0.604 7.400 19631 Z= 0.314 Chirality : 0.044 0.151 2105 Planarity : 0.005 0.048 2388 Dihedral : 13.905 68.394 2206 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.38 % Allowed : 13.44 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1610 helix: 1.35 (0.19), residues: 693 sheet: 0.62 (0.33), residues: 224 loop : -0.03 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 241 HIS 0.008 0.001 HIS B 258 PHE 0.016 0.002 PHE A1129 TYR 0.023 0.002 TYR A 479 ARG 0.007 0.001 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 672) hydrogen bonds : angle 5.10573 ( 1885) covalent geometry : bond 0.00562 (14363) covalent geometry : angle 0.60386 (19631) *********************** 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 235 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.5967 (mp) REVERT: A 226 GLN cc_start: 0.7180 (mt0) cc_final: 0.6654 (pt0) REVERT: A 248 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5901 (mp0) REVERT: A 361 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6566 (ttm-80) REVERT: A 371 LYS cc_start: 0.8425 (ptmt) cc_final: 0.7681 (ptpp) REVERT: A 385 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5569 (mp) REVERT: A 581 ASP cc_start: 0.7015 (m-30) cc_final: 0.6700 (p0) REVERT: A 598 VAL cc_start: 0.6703 (m) cc_final: 0.6350 (p) REVERT: A 1121 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: A 1164 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6854 (t80) REVERT: B 85 GLN cc_start: 0.6856 (mp10) cc_final: 0.6497 (mp10) REVERT: B 185 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5417 (mt) REVERT: B 231 ILE cc_start: 0.6132 (mm) cc_final: 0.5671 (mt) REVERT: B 394 GLU cc_start: 0.8005 (tp30) cc_final: 0.7731 (tp30) REVERT: B 421 MET cc_start: 0.8025 (ptm) cc_final: 0.7138 (pp-130) REVERT: B 450 ASN cc_start: 0.6765 (OUTLIER) cc_final: 0.6462 (p0) REVERT: C 180 LYS cc_start: 0.2858 (tppt) cc_final: 0.2591 (tppt) REVERT: C 400 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6481 (tm-30) REVERT: C 422 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5636 (mp10) REVERT: C 427 GLN cc_start: 0.6546 (mt0) cc_final: 0.6090 (mp10) REVERT: C 449 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4659 (mm-30) REVERT: C 466 MET cc_start: 0.8052 (ttm) cc_final: 0.7579 (ttm) REVERT: C 469 SER cc_start: 0.8226 (t) cc_final: 0.7732 (p) outliers start: 48 outliers final: 29 residues processed: 221 average time/residue: 1.5575 time to fit residues: 377.0256 Evaluate side-chains 221 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 3.035 ------------------------------------------------------------------------------- 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 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 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 123 GLU Chi-restraints excluded: chain B residue 185 LEU 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 336 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 450 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 B 427 GLN ** 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 = 0.4298 r_free = 0.4298 target = 0.179949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134098 restraints weight = 13988.445| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.98 r_work: 0.3681 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14363 Z= 0.152 Angle : 0.535 7.698 19631 Z= 0.281 Chirality : 0.040 0.143 2105 Planarity : 0.004 0.047 2388 Dihedral : 13.780 60.982 2206 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.81 % Allowed : 14.50 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1610 helix: 1.51 (0.19), residues: 693 sheet: 0.80 (0.32), residues: 232 loop : 0.08 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 241 HIS 0.009 0.001 HIS B 258 PHE 0.014 0.001 PHE C 403 TYR 0.024 0.002 TYR A 479 ARG 0.007 0.000 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 672) hydrogen bonds : angle 4.94313 ( 1885) covalent geometry : bond 0.00349 (14363) covalent geometry : angle 0.53547 (19631) *********************** 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 223 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7800 (m-30) cc_final: 0.7573 (m-30) REVERT: A 158 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5777 (mp) REVERT: A 226 GLN cc_start: 0.7001 (mt0) cc_final: 0.6477 (pt0) REVERT: A 248 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: A 361 ARG cc_start: 0.6842 (ttm-80) cc_final: 0.6407 (ttm-80) REVERT: A 371 LYS cc_start: 0.8398 (ptmt) cc_final: 0.7627 (ptpp) REVERT: A 385 ILE cc_start: 0.6243 (OUTLIER) cc_final: 0.5488 (mp) REVERT: A 581 ASP cc_start: 0.6957 (m-30) cc_final: 0.6718 (p0) REVERT: A 1164 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6694 (t80) REVERT: B 85 GLN cc_start: 0.6844 (mp10) cc_final: 0.6543 (mp10) REVERT: B 231 ILE cc_start: 0.6087 (mm) cc_final: 0.5642 (mt) REVERT: B 322 LEU cc_start: 0.6505 (mp) cc_final: 0.6284 (mt) REVERT: B 394 GLU cc_start: 0.7982 (tp30) cc_final: 0.7716 (tp30) REVERT: B 421 MET cc_start: 0.7997 (ptm) cc_final: 0.7108 (pp-130) REVERT: B 450 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6497 (p0) REVERT: C 180 LYS cc_start: 0.2721 (tppt) cc_final: 0.2512 (tppt) REVERT: C 400 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6468 (tm-30) REVERT: C 422 GLN cc_start: 0.6301 (mm-40) cc_final: 0.5630 (mp10) REVERT: C 427 GLN cc_start: 0.6495 (mt0) cc_final: 0.6066 (mp10) REVERT: C 449 GLU cc_start: 0.4911 (mt-10) cc_final: 0.4555 (mm-30) REVERT: C 465 MET cc_start: 0.7375 (mmt) cc_final: 0.7130 (mmm) REVERT: C 466 MET cc_start: 0.7983 (ttm) cc_final: 0.7489 (ttm) REVERT: C 469 SER cc_start: 0.8190 (t) cc_final: 0.7698 (p) outliers start: 40 outliers final: 27 residues processed: 213 average time/residue: 1.3423 time to fit residues: 312.7769 Evaluate side-chains 216 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 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 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 261 GLN 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 B residue 450 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 121 optimal weight: 0.4980 chunk 133 optimal weight: 0.0030 chunk 113 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 142 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 161 optimal weight: 0.0570 overall best weight: 0.1546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 HIS ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 313 HIS B 427 GLN C 85 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.184895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140442 restraints weight = 14051.684| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.99 r_work: 0.3757 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14363 Z= 0.107 Angle : 0.488 8.263 19631 Z= 0.258 Chirality : 0.038 0.137 2105 Planarity : 0.004 0.046 2388 Dihedral : 13.487 59.504 2206 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.90 % Allowed : 15.20 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1610 helix: 1.74 (0.20), residues: 700 sheet: 0.88 (0.32), residues: 240 loop : 0.21 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 241 HIS 0.010 0.001 HIS B 258 PHE 0.016 0.001 PHE C 403 TYR 0.019 0.001 TYR C 193 ARG 0.008 0.000 ARG A 927 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 672) hydrogen bonds : angle 4.67942 ( 1885) covalent geometry : bond 0.00228 (14363) covalent geometry : angle 0.48792 (19631) *********************** 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 219 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7714 (m-30) cc_final: 0.7454 (m-30) REVERT: A 226 GLN cc_start: 0.6844 (mt0) cc_final: 0.6418 (pt0) REVERT: A 248 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5687 (mp0) REVERT: A 361 ARG cc_start: 0.6789 (ttm-80) cc_final: 0.6377 (ttm-80) REVERT: A 371 LYS cc_start: 0.8367 (ptmt) cc_final: 0.7444 (ptpp) REVERT: B 85 GLN cc_start: 0.6915 (mp10) cc_final: 0.6617 (mp10) REVERT: B 322 LEU cc_start: 0.6431 (mp) cc_final: 0.6203 (mt) REVERT: B 394 GLU cc_start: 0.7845 (tp30) cc_final: 0.7592 (tp30) REVERT: B 421 MET cc_start: 0.8008 (ptm) cc_final: 0.7127 (pp-130) REVERT: C 180 LYS cc_start: 0.2733 (tppt) cc_final: 0.2529 (tppt) REVERT: C 400 GLN cc_start: 0.6720 (mm-40) cc_final: 0.6262 (tm-30) REVERT: C 422 GLN cc_start: 0.6175 (mm-40) cc_final: 0.5582 (mp10) REVERT: C 427 GLN cc_start: 0.6387 (mt0) cc_final: 0.5961 (mp10) REVERT: C 449 GLU cc_start: 0.4866 (mt-10) cc_final: 0.4503 (mm-30) REVERT: C 465 MET cc_start: 0.7385 (mmt) cc_final: 0.7125 (mmm) REVERT: C 466 MET cc_start: 0.7929 (ttm) cc_final: 0.7434 (ttm) REVERT: C 469 SER cc_start: 0.8131 (t) cc_final: 0.7686 (p) outliers start: 27 outliers final: 11 residues processed: 211 average time/residue: 1.3409 time to fit residues: 308.7628 Evaluate side-chains 189 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU 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 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 C residue 128 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.0270 chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 258 HIS B 313 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.178957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141031 restraints weight = 13947.975| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.18 r_work: 0.3646 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14363 Z= 0.208 Angle : 0.585 8.373 19631 Z= 0.303 Chirality : 0.043 0.147 2105 Planarity : 0.005 0.046 2388 Dihedral : 13.740 59.943 2205 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.62 % Allowed : 16.19 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1610 helix: 1.54 (0.19), residues: 695 sheet: 0.79 (0.32), residues: 239 loop : 0.10 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 241 HIS 0.016 0.001 HIS B 258 PHE 0.014 0.002 PHE A1129 TYR 0.037 0.002 TYR A 479 ARG 0.007 0.001 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 672) hydrogen bonds : angle 4.92988 ( 1885) covalent geometry : bond 0.00488 (14363) covalent geometry : angle 0.58477 (19631) ********************** 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 202 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7851 (m-30) cc_final: 0.7626 (m-30) REVERT: A 134 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.7072 (p0) REVERT: A 158 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5925 (mp) REVERT: A 226 GLN cc_start: 0.6991 (mt0) cc_final: 0.6513 (pt0) REVERT: A 248 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5898 (mp0) REVERT: A 361 ARG cc_start: 0.6935 (ttm-80) cc_final: 0.6513 (ttm-80) REVERT: A 371 LYS cc_start: 0.8401 (ptmt) cc_final: 0.7674 (ptpp) REVERT: A 581 ASP cc_start: 0.6969 (m-30) cc_final: 0.6659 (p0) REVERT: A 1121 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: B 85 GLN cc_start: 0.6993 (mp10) cc_final: 0.6695 (mp10) REVERT: B 231 ILE cc_start: 0.6315 (mm) cc_final: 0.6016 (mt) REVERT: B 394 GLU cc_start: 0.7990 (tp30) cc_final: 0.7742 (tp30) REVERT: B 421 MET cc_start: 0.8037 (ptm) cc_final: 0.7169 (pp-130) REVERT: B 427 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6424 (pt0) REVERT: C 180 LYS cc_start: 0.2841 (tppt) cc_final: 0.2626 (tppt) REVERT: C 400 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6550 (tm-30) REVERT: C 422 GLN cc_start: 0.6280 (mm-40) cc_final: 0.5592 (mp10) REVERT: C 427 GLN cc_start: 0.6544 (mt0) cc_final: 0.6108 (mp10) REVERT: C 449 GLU cc_start: 0.5047 (mt-10) cc_final: 0.4671 (mm-30) REVERT: C 466 MET cc_start: 0.8050 (ttm) cc_final: 0.7547 (ttm) REVERT: C 469 SER cc_start: 0.8171 (t) cc_final: 0.7700 (p) outliers start: 23 outliers final: 12 residues processed: 196 average time/residue: 1.3913 time to fit residues: 299.0116 Evaluate side-chains 193 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 776 ASP 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 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 427 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 85 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133175 restraints weight = 14042.436| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.99 r_work: 0.3677 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 14363 Z= 0.237 Angle : 1.016 59.193 19631 Z= 0.570 Chirality : 0.043 0.506 2105 Planarity : 0.006 0.145 2388 Dihedral : 13.749 59.928 2205 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.55 % Allowed : 16.33 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1610 helix: 1.52 (0.19), residues: 695 sheet: 0.78 (0.32), residues: 239 loop : 0.09 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 241 HIS 0.015 0.001 HIS B 258 PHE 0.013 0.001 PHE A1129 TYR 0.031 0.002 TYR A 479 ARG 0.007 0.000 ARG A 818 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 672) hydrogen bonds : angle 4.92990 ( 1885) covalent geometry : bond 0.00501 (14363) covalent geometry : angle 1.01627 (19631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15309.49 seconds wall clock time: 269 minutes 43.07 seconds (16183.07 seconds total)