Starting phenix.real_space_refine on Thu Jun 12 12:14:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggf_51330/06_2025/9ggf_51330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggf_51330/06_2025/9ggf_51330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ggf_51330/06_2025/9ggf_51330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggf_51330/06_2025/9ggf_51330.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggf_51330/06_2025/9ggf_51330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggf_51330/06_2025/9ggf_51330.cif" } resolution = 2.65 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= 0.002 sd= 0.975 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 8745 2.51 5 N 2446 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 13925 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7425 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 62, 'TRANS': 869} 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: 10.47, per 1000 atoms: 0.75 Number of scatterers: 13925 At special positions: 0 Unit cell: (94.875, 104.775, 144.375, 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 2612 8.00 N 2446 7.00 C 8745 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: 5.02 Conformation dependent library (CDL) restraints added in 2.2 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 47.0% alpha, 14.4% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.223A pdb=" N GLN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix 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 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.570A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 6.651A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.583A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 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 432 removed outlier: 3.928A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.633A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.611A pdb=" N LEU A 558 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.840A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 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 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.751A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 874 through 878 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 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 986 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.719A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.724A 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 120 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.070A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 265 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: 3.657A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (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: 4.091A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.598A pdb=" N PHE B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.806A 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: 4.154A 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 353 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.699A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.814A 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 187 removed outlier: 3.689A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.193A 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: 4.823A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 7.550A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.596A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.111A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.052A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 307 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER C 337 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN C 305 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN C 339 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU C 303 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP C 341 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU C 301 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB2, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.122A pdb=" N LYS C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.192A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3966 1.33 - 1.45: 2578 1.45 - 1.57: 7610 1.57 - 1.69: 79 1.69 - 1.81: 126 Bond restraints: 14359 Sorted by residual: bond pdb=" C6 DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 1.375 1.335 0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" C4 DCP A1302 " pdb=" C5 DCP A1302 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" O1B DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.477 1.510 -0.033 1.10e-02 8.26e+03 9.26e+00 bond pdb=" O1A DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.477 1.502 -0.025 1.00e-02 1.00e+04 6.43e+00 bond pdb=" CA SER B 457 " pdb=" C SER B 457 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.28e-02 6.10e+03 5.86e+00 ... (remaining 14354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 19588 3.19 - 6.37: 34 6.37 - 9.56: 1 9.56 - 12.74: 0 12.74 - 15.93: 2 Bond angle restraints: 19625 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 123.94 15.93 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 136.83 123.19 13.64 1.00e+00 1.00e+00 1.86e+02 angle pdb=" O1G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 110.47 103.56 6.91 1.64e+00 3.70e-01 1.77e+01 angle pdb=" C2' DCP A1302 " pdb=" C1' DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 113.92 108.85 5.07 1.28e+00 6.12e-01 1.57e+01 angle pdb=" N GLU C 449 " pdb=" CA GLU C 449 " pdb=" C GLU C 449 " ideal model delta sigma weight residual 111.14 115.09 -3.95 1.08e+00 8.57e-01 1.34e+01 ... (remaining 19620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7916 17.97 - 35.95: 378 35.95 - 53.92: 135 53.92 - 71.89: 24 71.89 - 89.87: 3 Dihedral angle restraints: 8456 sinusoidal: 3744 harmonic: 4712 Sorted by residual: dihedral pdb=" CA VAL A 196 " pdb=" C VAL A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 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 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" N GLN A 564 " pdb=" CA GLN A 564 " pdb=" CB GLN A 564 " pdb=" CG GLN A 564 " ideal model delta sinusoidal sigma weight residual -60.00 -117.44 57.44 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 8453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1306 0.027 - 0.053: 535 0.053 - 0.080: 127 0.080 - 0.107: 100 0.107 - 0.134: 33 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 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 -2.55 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 840 " pdb=" N ILE A 840 " pdb=" C ILE A 840 " pdb=" CB ILE A 840 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 2098 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+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 GLY A 782 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 783 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 783 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 783 " 0.022 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 3.79e-02 2.30e+00 pdb=" N PRO A1200 " 0.066 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 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 15 2.36 - 2.99: 6755 2.99 - 3.63: 20606 3.63 - 4.26: 33058 4.26 - 4.90: 54631 Nonbonded interactions: 115065 Sorted by model distance: nonbonded pdb=" OD2 ASP A1135 " pdb="CA CA A1301 " model vdw 1.725 2.510 nonbonded pdb="CA CA A1301 " pdb=" O1B DCP A1302 " model vdw 1.815 2.510 nonbonded pdb=" OG SER A 272 " pdb=" O VAL A 844 " model vdw 2.202 3.040 nonbonded pdb="CA CA A1301 " pdb=" O2G DCP A1302 " model vdw 2.250 2.510 nonbonded pdb=" O SER C 117 " pdb=" NH1 ARG C 122 " model vdw 2.291 3.120 ... (remaining 115060 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.840 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: 2.230 Check model and map are aligned: 0.090 Set scattering table: 0.160 Process input model: 43.910 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:17.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.002 0.042 14359 Z= 0.137 Angle : 0.484 15.925 19625 Z= 0.297 Chirality : 0.038 0.134 2101 Planarity : 0.004 0.042 2388 Dihedral : 12.164 89.866 5418 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.56 % Allowed : 2.54 % Favored : 96.90 % 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: 1.34 (0.21), residues: 1609 helix: 1.64 (0.20), residues: 700 sheet: 0.92 (0.33), residues: 236 loop : 0.18 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 312 HIS 0.003 0.001 HIS B 77 PHE 0.015 0.001 PHE C 403 TYR 0.010 0.001 TYR A 150 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.15731 ( 675) hydrogen bonds : angle 6.44540 ( 1894) covalent geometry : bond 0.00247 (14359) covalent geometry : angle 0.48424 (19625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 316 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6378 (ttt-90) cc_final: 0.5669 (ttp80) REVERT: A 193 ARG cc_start: 0.7401 (mtm180) cc_final: 0.6177 (mmp80) REVERT: A 232 ARG cc_start: 0.6691 (mtt180) cc_final: 0.6128 (mtm180) REVERT: A 459 MET cc_start: 0.8211 (tpp) cc_final: 0.7788 (tmm) REVERT: A 773 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7544 (mppt) REVERT: A 856 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 1089 GLN cc_start: 0.7272 (mt0) cc_final: 0.7028 (mp10) REVERT: B 134 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7507 (mmtt) REVERT: B 250 GLN cc_start: 0.7203 (mt0) cc_final: 0.6943 (mm-40) REVERT: B 461 THR cc_start: 0.6800 (p) cc_final: 0.6576 (p) REVERT: C 407 LEU cc_start: 0.7983 (mt) cc_final: 0.7780 (mm) REVERT: C 411 ILE cc_start: 0.8431 (mt) cc_final: 0.8214 (mt) outliers start: 8 outliers final: 3 residues processed: 323 average time/residue: 1.6559 time to fit residues: 584.0212 Evaluate side-chains 193 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain C residue 128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.0030 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.0070 chunk 79 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 overall best weight: 0.8412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A1098 ASN A1102 GLN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 272 ASN B 330 ASN B 397 GLN C 184 ASN C 187 HIS C 287 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130396 restraints weight = 14679.505| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.15 r_work: 0.3613 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14359 Z= 0.135 Angle : 0.540 11.466 19625 Z= 0.280 Chirality : 0.041 0.175 2101 Planarity : 0.005 0.050 2388 Dihedral : 13.774 94.855 2206 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.47 % Allowed : 11.77 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.21), residues: 1609 helix: 1.69 (0.20), residues: 704 sheet: 1.04 (0.33), residues: 234 loop : 0.25 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 241 HIS 0.008 0.001 HIS C 187 PHE 0.016 0.002 PHE C 403 TYR 0.020 0.002 TYR A1166 ARG 0.008 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 675) hydrogen bonds : angle 4.98971 ( 1894) covalent geometry : bond 0.00311 (14359) covalent geometry : angle 0.53977 (19625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.5996 (ttt-90) cc_final: 0.5056 (ttp80) REVERT: A 193 ARG cc_start: 0.7159 (mtm180) cc_final: 0.5154 (mmp80) REVERT: A 232 ARG cc_start: 0.6417 (mtt180) cc_final: 0.5550 (mtm180) REVERT: A 459 MET cc_start: 0.8585 (tpp) cc_final: 0.7920 (tmm) REVERT: A 773 LYS cc_start: 0.7417 (mmmt) cc_final: 0.6645 (mppt) REVERT: A 1089 GLN cc_start: 0.7144 (mt0) cc_final: 0.6679 (mp10) REVERT: B 134 LYS cc_start: 0.7353 (ttpt) cc_final: 0.6282 (mmtt) REVERT: B 250 GLN cc_start: 0.7436 (mt0) cc_final: 0.6720 (mm-40) REVERT: B 325 ARG cc_start: 0.6161 (mtt90) cc_final: 0.5863 (mtm110) REVERT: C 236 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: C 249 ASN cc_start: 0.5854 (m-40) cc_final: 0.5518 (m110) REVERT: C 325 ARG cc_start: 0.5471 (mtm110) cc_final: 0.4812 (mmm160) REVERT: C 334 CYS cc_start: 0.6684 (m) cc_final: 0.5866 (t) REVERT: C 370 LYS cc_start: 0.8276 (mmtm) cc_final: 0.8072 (mttt) REVERT: C 407 LEU cc_start: 0.7619 (mt) cc_final: 0.7392 (mm) outliers start: 35 outliers final: 12 residues processed: 214 average time/residue: 1.6732 time to fit residues: 392.2656 Evaluate side-chains 183 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 42 optimal weight: 0.0270 chunk 160 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 184 ASN C 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.166708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128538 restraints weight = 14854.535| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.12 r_work: 0.3592 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14359 Z= 0.131 Angle : 0.520 10.147 19625 Z= 0.268 Chirality : 0.040 0.172 2101 Planarity : 0.005 0.051 2388 Dihedral : 13.612 86.566 2206 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.26 % Allowed : 12.90 % Favored : 84.85 % 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: 1.45 (0.21), residues: 1609 helix: 1.70 (0.20), residues: 703 sheet: 1.04 (0.32), residues: 247 loop : 0.23 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 241 HIS 0.004 0.001 HIS C 454 PHE 0.019 0.002 PHE B 242 TYR 0.020 0.002 TYR A1166 ARG 0.007 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 675) hydrogen bonds : angle 4.80877 ( 1894) covalent geometry : bond 0.00301 (14359) covalent geometry : angle 0.51951 (19625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.5979 (ttt-90) cc_final: 0.5023 (ttp80) REVERT: A 193 ARG cc_start: 0.7171 (mtm180) cc_final: 0.5217 (mmp80) REVERT: A 232 ARG cc_start: 0.6353 (mtt180) cc_final: 0.5529 (mtm180) REVERT: A 263 GLU cc_start: 0.7360 (mp0) cc_final: 0.6933 (mp0) REVERT: A 459 MET cc_start: 0.8506 (tpp) cc_final: 0.7839 (tmm) REVERT: A 494 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7548 (pm20) REVERT: A 559 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5182 (mt) REVERT: A 773 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6557 (mppt) REVERT: A 776 ASP cc_start: 0.7923 (t0) cc_final: 0.7549 (t0) REVERT: A 1089 GLN cc_start: 0.7074 (mt0) cc_final: 0.6650 (mp10) REVERT: B 134 LYS cc_start: 0.7408 (ttpt) cc_final: 0.6255 (mmtt) REVERT: B 250 GLN cc_start: 0.7266 (mt0) cc_final: 0.6556 (mm-40) REVERT: B 308 ASP cc_start: 0.7431 (p0) cc_final: 0.7149 (p0) REVERT: C 183 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: C 236 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: C 249 ASN cc_start: 0.5824 (m-40) cc_final: 0.5563 (m110) REVERT: C 325 ARG cc_start: 0.5633 (mtm110) cc_final: 0.4879 (mmm160) REVERT: C 334 CYS cc_start: 0.6774 (m) cc_final: 0.5907 (t) REVERT: C 370 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8083 (mttt) outliers start: 32 outliers final: 15 residues processed: 195 average time/residue: 1.3067 time to fit residues: 279.1991 Evaluate side-chains 186 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 86 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 148 optimal weight: 0.1980 chunk 115 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 736 ASN A 906 HIS A 922 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 397 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122036 restraints weight = 14780.023| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.15 r_work: 0.3530 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14359 Z= 0.263 Angle : 0.656 10.734 19625 Z= 0.333 Chirality : 0.046 0.198 2101 Planarity : 0.006 0.067 2388 Dihedral : 13.948 84.030 2204 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.96 % Allowed : 12.47 % Favored : 84.57 % 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: 0.88 (0.20), residues: 1609 helix: 1.12 (0.19), residues: 704 sheet: 0.83 (0.31), residues: 247 loop : 0.04 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 312 HIS 0.006 0.001 HIS A 805 PHE 0.021 0.002 PHE B 242 TYR 0.020 0.003 TYR B 291 ARG 0.006 0.001 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 675) hydrogen bonds : angle 5.08834 ( 1894) covalent geometry : bond 0.00631 (14359) covalent geometry : angle 0.65593 (19625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6190 (ttt-90) cc_final: 0.5010 (ttp80) REVERT: A 193 ARG cc_start: 0.7209 (mtm180) cc_final: 0.5255 (mmp80) REVERT: A 263 GLU cc_start: 0.7486 (mp0) cc_final: 0.7052 (mp0) REVERT: A 459 MET cc_start: 0.8518 (tpp) cc_final: 0.7852 (tmm) REVERT: A 494 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: A 776 ASP cc_start: 0.8033 (t0) cc_final: 0.7715 (t0) REVERT: A 922 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6120 (mt0) REVERT: A 1089 GLN cc_start: 0.6991 (mt0) cc_final: 0.6571 (mp10) REVERT: A 1164 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6427 (t80) REVERT: B 134 LYS cc_start: 0.7398 (ttpt) cc_final: 0.6002 (mmtt) REVERT: B 250 GLN cc_start: 0.7193 (mt0) cc_final: 0.6428 (mm-40) REVERT: B 325 ARG cc_start: 0.6028 (mtm110) cc_final: 0.5651 (mtm110) REVERT: C 122 ARG cc_start: 0.6636 (mtm-85) cc_final: 0.6356 (mtt-85) REVERT: C 236 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: C 313 HIS cc_start: 0.5664 (t-90) cc_final: 0.4814 (m90) REVERT: C 325 ARG cc_start: 0.5597 (mtm110) cc_final: 0.4811 (mmm160) REVERT: C 334 CYS cc_start: 0.6963 (m) cc_final: 0.6004 (t) REVERT: C 370 LYS cc_start: 0.8328 (mmtm) cc_final: 0.7976 (mttt) REVERT: C 463 LYS cc_start: 0.7997 (mttm) cc_final: 0.7793 (mtmt) outliers start: 42 outliers final: 20 residues processed: 206 average time/residue: 1.3649 time to fit residues: 307.9325 Evaluate side-chains 195 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 922 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.164828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126078 restraints weight = 14807.009| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.14 r_work: 0.3573 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14359 Z= 0.123 Angle : 0.527 9.608 19625 Z= 0.270 Chirality : 0.040 0.170 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.713 83.613 2204 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.40 % Allowed : 13.67 % Favored : 83.93 % 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: 1.25 (0.21), residues: 1609 helix: 1.50 (0.20), residues: 703 sheet: 1.08 (0.32), residues: 231 loop : 0.13 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 PHE 0.022 0.001 PHE A 88 TYR 0.021 0.002 TYR A1166 ARG 0.008 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 675) hydrogen bonds : angle 4.74243 ( 1894) covalent geometry : bond 0.00281 (14359) covalent geometry : angle 0.52702 (19625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.604 Fit side-chains REVERT: A 177 ARG cc_start: 0.6111 (ttt-90) cc_final: 0.4996 (ttp80) REVERT: A 193 ARG cc_start: 0.7120 (mtm180) cc_final: 0.5211 (mmp80) REVERT: A 263 GLU cc_start: 0.7411 (mp0) cc_final: 0.6961 (mp0) REVERT: A 459 MET cc_start: 0.8465 (tpp) cc_final: 0.7839 (tmm) REVERT: A 494 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7494 (pm20) REVERT: A 559 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.4979 (mt) REVERT: A 922 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6191 (mt0) REVERT: A 1089 GLN cc_start: 0.7043 (mt0) cc_final: 0.6603 (mp10) REVERT: B 134 LYS cc_start: 0.7306 (ttpt) cc_final: 0.5931 (mmtt) REVERT: B 250 GLN cc_start: 0.7164 (mt0) cc_final: 0.6420 (mm-40) REVERT: B 308 ASP cc_start: 0.7565 (p0) cc_final: 0.7261 (p0) REVERT: C 89 ASP cc_start: 0.7150 (t0) cc_final: 0.6813 (m-30) REVERT: C 183 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: C 206 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7940 (p90) REVERT: C 236 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: C 313 HIS cc_start: 0.5569 (t-90) cc_final: 0.4771 (m90) REVERT: C 325 ARG cc_start: 0.5645 (mtm110) cc_final: 0.4670 (mmm160) REVERT: C 334 CYS cc_start: 0.6752 (m) cc_final: 0.5832 (t) REVERT: C 370 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7987 (mttt) outliers start: 34 outliers final: 11 residues processed: 188 average time/residue: 1.6893 time to fit residues: 345.0489 Evaluate side-chains 180 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 922 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125111 restraints weight = 14981.539| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.15 r_work: 0.3567 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14359 Z= 0.143 Angle : 0.535 11.085 19625 Z= 0.274 Chirality : 0.041 0.164 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.665 83.404 2204 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.26 % Allowed : 14.45 % Favored : 83.30 % 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: 1.21 (0.20), residues: 1609 helix: 1.58 (0.20), residues: 697 sheet: 1.01 (0.33), residues: 223 loop : 0.02 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 241 HIS 0.006 0.001 HIS C 454 PHE 0.020 0.002 PHE B 242 TYR 0.021 0.002 TYR A1166 ARG 0.008 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 675) hydrogen bonds : angle 4.73465 ( 1894) covalent geometry : bond 0.00334 (14359) covalent geometry : angle 0.53540 (19625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.876 Fit side-chains REVERT: A 177 ARG cc_start: 0.6165 (ttt-90) cc_final: 0.5065 (ttp80) REVERT: A 193 ARG cc_start: 0.7145 (mtm180) cc_final: 0.5220 (mmp80) REVERT: A 263 GLU cc_start: 0.7425 (mp0) cc_final: 0.6957 (mp0) REVERT: A 459 MET cc_start: 0.8463 (tpp) cc_final: 0.7834 (tmm) REVERT: A 494 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7436 (pm20) REVERT: A 922 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5694 (mt0) REVERT: A 1089 GLN cc_start: 0.7057 (mt0) cc_final: 0.6574 (mp10) REVERT: B 134 LYS cc_start: 0.7347 (ttpt) cc_final: 0.5950 (mmtt) REVERT: B 250 GLN cc_start: 0.7160 (mt0) cc_final: 0.6403 (mm-40) REVERT: B 308 ASP cc_start: 0.7533 (p0) cc_final: 0.7213 (p0) REVERT: B 314 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6824 (ttp) REVERT: B 325 ARG cc_start: 0.6236 (mtm110) cc_final: 0.5917 (mtm110) REVERT: C 89 ASP cc_start: 0.7140 (t0) cc_final: 0.6812 (m-30) REVERT: C 236 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: C 325 ARG cc_start: 0.5692 (mtm110) cc_final: 0.4737 (mmm160) REVERT: C 334 CYS cc_start: 0.6795 (m) cc_final: 0.5868 (t) REVERT: C 370 LYS cc_start: 0.8315 (mmtm) cc_final: 0.7997 (mttt) outliers start: 32 outliers final: 20 residues processed: 186 average time/residue: 2.0142 time to fit residues: 410.5223 Evaluate side-chains 184 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 922 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.164564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125624 restraints weight = 14962.526| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.16 r_work: 0.3573 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14359 Z= 0.134 Angle : 0.539 12.357 19625 Z= 0.275 Chirality : 0.040 0.173 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.625 83.040 2204 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.82 % Allowed : 14.02 % Favored : 83.16 % 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: 1.25 (0.20), residues: 1609 helix: 1.63 (0.20), residues: 697 sheet: 1.01 (0.33), residues: 223 loop : 0.02 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 PHE 0.024 0.002 PHE B 242 TYR 0.022 0.002 TYR A1166 ARG 0.009 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 675) hydrogen bonds : angle 4.70299 ( 1894) covalent geometry : bond 0.00313 (14359) covalent geometry : angle 0.53874 (19625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.440 Fit side-chains REVERT: A 177 ARG cc_start: 0.6136 (ttt-90) cc_final: 0.5039 (ttp80) REVERT: A 193 ARG cc_start: 0.7132 (mtm180) cc_final: 0.5199 (mmp80) REVERT: A 263 GLU cc_start: 0.7424 (mp0) cc_final: 0.6956 (mp0) REVERT: A 459 MET cc_start: 0.8464 (tpp) cc_final: 0.7844 (tmm) REVERT: A 494 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7385 (pm20) REVERT: A 559 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.4924 (mt) REVERT: A 1089 GLN cc_start: 0.7071 (mt0) cc_final: 0.6577 (mp10) REVERT: B 124 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6470 (pm20) REVERT: B 134 LYS cc_start: 0.7342 (ttpt) cc_final: 0.5957 (mmtt) REVERT: B 250 GLN cc_start: 0.7154 (mt0) cc_final: 0.6394 (mm-40) REVERT: B 308 ASP cc_start: 0.7530 (p0) cc_final: 0.7195 (p0) REVERT: B 314 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6852 (ttp) REVERT: B 325 ARG cc_start: 0.6175 (mtm110) cc_final: 0.5861 (mtm110) REVERT: B 465 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7440 (mpp) REVERT: C 89 ASP cc_start: 0.7170 (t0) cc_final: 0.6829 (m-30) REVERT: C 236 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: C 313 HIS cc_start: 0.5540 (t-90) cc_final: 0.4765 (m90) REVERT: C 325 ARG cc_start: 0.5651 (mtm110) cc_final: 0.4714 (mmm160) REVERT: C 334 CYS cc_start: 0.6731 (m) cc_final: 0.5789 (t) REVERT: C 370 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7992 (mttt) outliers start: 40 outliers final: 20 residues processed: 189 average time/residue: 1.4131 time to fit residues: 290.4460 Evaluate side-chains 190 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 chunk 160 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 736 ASN A 922 GLN A 983 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127689 restraints weight = 14878.772| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.14 r_work: 0.3593 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14359 Z= 0.112 Angle : 0.510 9.278 19625 Z= 0.264 Chirality : 0.039 0.153 2101 Planarity : 0.004 0.052 2388 Dihedral : 13.542 82.739 2204 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.47 % Allowed : 14.16 % Favored : 83.37 % 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: 1.33 (0.21), residues: 1609 helix: 1.73 (0.20), residues: 697 sheet: 0.99 (0.34), residues: 216 loop : 0.06 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 918 HIS 0.004 0.001 HIS C 454 PHE 0.023 0.002 PHE B 242 TYR 0.022 0.001 TYR A1166 ARG 0.009 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 675) hydrogen bonds : angle 4.61609 ( 1894) covalent geometry : bond 0.00254 (14359) covalent geometry : angle 0.50990 (19625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.438 Fit side-chains REVERT: A 177 ARG cc_start: 0.6094 (ttt-90) cc_final: 0.5020 (ttp80) REVERT: A 193 ARG cc_start: 0.7091 (mtm180) cc_final: 0.5178 (mmp80) REVERT: A 263 GLU cc_start: 0.7411 (mp0) cc_final: 0.6995 (mp0) REVERT: A 454 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: A 459 MET cc_start: 0.8459 (tpp) cc_final: 0.7852 (tmm) REVERT: A 494 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7351 (pm20) REVERT: A 559 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.4902 (mt) REVERT: A 1089 GLN cc_start: 0.7033 (mt0) cc_final: 0.6591 (mp10) REVERT: B 123 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: B 134 LYS cc_start: 0.7319 (ttpt) cc_final: 0.5943 (mmtt) REVERT: B 250 GLN cc_start: 0.7136 (mt0) cc_final: 0.6383 (mm-40) REVERT: B 261 GLN cc_start: 0.7825 (pt0) cc_final: 0.7139 (mm110) REVERT: B 325 ARG cc_start: 0.6142 (mtm110) cc_final: 0.5853 (mtm110) REVERT: B 465 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7367 (mpp) REVERT: C 89 ASP cc_start: 0.7152 (t0) cc_final: 0.6809 (m-30) REVERT: C 183 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: C 236 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: C 325 ARG cc_start: 0.5688 (mtm110) cc_final: 0.4738 (mmm160) REVERT: C 334 CYS cc_start: 0.6708 (m) cc_final: 0.5835 (t) REVERT: C 370 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8022 (mttt) outliers start: 35 outliers final: 17 residues processed: 192 average time/residue: 1.3596 time to fit residues: 284.9340 Evaluate side-chains 186 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 0.0270 chunk 13 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 922 GLN A 983 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.165189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126383 restraints weight = 14785.722| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.15 r_work: 0.3578 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14359 Z= 0.133 Angle : 0.548 12.135 19625 Z= 0.279 Chirality : 0.040 0.160 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.527 82.344 2204 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.18 % Allowed : 15.29 % Favored : 82.52 % 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: 1.33 (0.21), residues: 1609 helix: 1.69 (0.20), residues: 698 sheet: 0.99 (0.34), residues: 216 loop : 0.10 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 918 HIS 0.003 0.001 HIS A 805 PHE 0.024 0.002 PHE A 273 TYR 0.022 0.002 TYR A1166 ARG 0.009 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 675) hydrogen bonds : angle 4.66982 ( 1894) covalent geometry : bond 0.00313 (14359) covalent geometry : angle 0.54826 (19625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.469 Fit side-chains REVERT: A 177 ARG cc_start: 0.6149 (ttt-90) cc_final: 0.5064 (ttp80) REVERT: A 263 GLU cc_start: 0.7452 (mp0) cc_final: 0.7169 (mp0) REVERT: A 459 MET cc_start: 0.8468 (tpp) cc_final: 0.7891 (tmm) REVERT: A 494 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7422 (pm20) REVERT: A 1089 GLN cc_start: 0.7075 (mt0) cc_final: 0.6657 (mp10) REVERT: B 123 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: B 124 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6387 (pm20) REVERT: B 134 LYS cc_start: 0.7418 (ttpt) cc_final: 0.6046 (mmtt) REVERT: B 250 GLN cc_start: 0.7221 (mt0) cc_final: 0.6526 (mm-40) REVERT: B 325 ARG cc_start: 0.6132 (mtm110) cc_final: 0.5834 (mtm110) REVERT: B 465 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7381 (mpp) REVERT: C 89 ASP cc_start: 0.7215 (t0) cc_final: 0.6901 (m-30) REVERT: C 236 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: C 325 ARG cc_start: 0.5759 (mtm110) cc_final: 0.4942 (mmm160) REVERT: C 334 CYS cc_start: 0.6786 (m) cc_final: 0.5869 (t) REVERT: C 370 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8031 (mttt) REVERT: C 465 MET cc_start: 0.8301 (tpp) cc_final: 0.7959 (mmt) outliers start: 31 outliers final: 16 residues processed: 182 average time/residue: 1.3929 time to fit residues: 276.7028 Evaluate side-chains 181 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 0.4980 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 157 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 983 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.165093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126372 restraints weight = 14812.163| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.14 r_work: 0.3580 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14359 Z= 0.133 Angle : 0.544 13.338 19625 Z= 0.277 Chirality : 0.040 0.155 2101 Planarity : 0.005 0.051 2388 Dihedral : 13.527 81.989 2204 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.97 % Allowed : 15.57 % Favored : 82.45 % 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 (0.21), residues: 1609 helix: 1.67 (0.20), residues: 698 sheet: 0.98 (0.34), residues: 216 loop : 0.11 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 918 HIS 0.003 0.001 HIS A 805 PHE 0.025 0.002 PHE A 273 TYR 0.022 0.002 TYR A1166 ARG 0.009 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 675) hydrogen bonds : angle 4.68555 ( 1894) covalent geometry : bond 0.00311 (14359) covalent geometry : angle 0.54400 (19625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.576 Fit side-chains REVERT: A 177 ARG cc_start: 0.6204 (ttt-90) cc_final: 0.5094 (ttp80) REVERT: A 263 GLU cc_start: 0.7444 (mp0) cc_final: 0.7163 (mp0) REVERT: A 459 MET cc_start: 0.8469 (tpp) cc_final: 0.7906 (tmm) REVERT: A 494 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7401 (pm20) REVERT: A 558 LEU cc_start: 0.6593 (tm) cc_final: 0.6390 (tp) REVERT: A 559 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.5031 (mt) REVERT: A 1089 GLN cc_start: 0.7121 (mt0) cc_final: 0.6679 (mp10) REVERT: B 123 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: B 124 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: B 134 LYS cc_start: 0.7417 (ttpt) cc_final: 0.6022 (mmtt) REVERT: B 250 GLN cc_start: 0.7215 (mt0) cc_final: 0.6514 (mm-40) REVERT: B 261 GLN cc_start: 0.7790 (pt0) cc_final: 0.7197 (mp-120) REVERT: B 325 ARG cc_start: 0.6078 (mtm110) cc_final: 0.5703 (mtm110) REVERT: B 465 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7327 (mpp) REVERT: C 89 ASP cc_start: 0.7212 (t0) cc_final: 0.6904 (m-30) REVERT: C 236 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: C 325 ARG cc_start: 0.5673 (mtm110) cc_final: 0.4868 (mmm160) REVERT: C 334 CYS cc_start: 0.6803 (m) cc_final: 0.5883 (t) REVERT: C 370 LYS cc_start: 0.8345 (mmtm) cc_final: 0.8034 (mttt) outliers start: 28 outliers final: 17 residues processed: 184 average time/residue: 1.5410 time to fit residues: 310.5787 Evaluate side-chains 183 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 983 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125556 restraints weight = 15054.791| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.18 r_work: 0.3563 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14359 Z= 0.152 Angle : 0.570 13.038 19625 Z= 0.289 Chirality : 0.041 0.162 2101 Planarity : 0.005 0.051 2388 Dihedral : 13.554 81.894 2204 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.97 % Allowed : 15.57 % Favored : 82.45 % 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: 1609 helix: 1.55 (0.20), residues: 698 sheet: 0.99 (0.34), residues: 216 loop : 0.08 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 918 HIS 0.004 0.001 HIS A 805 PHE 0.026 0.002 PHE B 242 TYR 0.023 0.002 TYR B 432 ARG 0.009 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 675) hydrogen bonds : angle 4.74478 ( 1894) covalent geometry : bond 0.00358 (14359) covalent geometry : angle 0.56976 (19625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12483.76 seconds wall clock time: 219 minutes 3.88 seconds (13143.88 seconds total)