Starting phenix.real_space_refine on Thu Sep 18 04:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggf_51330/09_2025/9ggf_51330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggf_51330/09_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_51330/09_2025/9ggf_51330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggf_51330/09_2025/9ggf_51330.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggf_51330/09_2025/9ggf_51330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggf_51330/09_2025/9ggf_51330.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.92, per 1000 atoms: 0.28 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: 1.53 Conformation dependent library (CDL) restraints added in 729.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.88 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: 3.10 Time building geometry restraints manager: 1.85 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (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 ARG 0.003 0.000 ARG B 456 TYR 0.010 0.001 TYR A 150 PHE 0.015 0.001 PHE C 403 TRP 0.009 0.001 TRP A 312 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00247 (14359) covalent geometry : angle 0.48424 (19625) hydrogen bonds : bond 0.15731 ( 675) hydrogen bonds : angle 6.44540 ( 1894) *********************** 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 : 0.549 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: 0.7128 time to fit residues: 249.5985 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 : 0.521 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 A1134 HIS B 258 HIS B 272 ASN B 287 ASN B 330 ASN B 397 GLN 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 = 0.3983 r_free = 0.3983 target = 0.162564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123838 restraints weight = 14857.215| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.14 r_work: 0.3552 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14359 Z= 0.246 Angle : 0.647 11.552 19625 Z= 0.332 Chirality : 0.046 0.168 2101 Planarity : 0.006 0.053 2388 Dihedral : 14.104 98.333 2206 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.96 % Allowed : 11.56 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.20), residues: 1609 helix: 1.20 (0.19), residues: 704 sheet: 0.93 (0.32), residues: 237 loop : 0.05 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1071 TYR 0.018 0.002 TYR A1166 PHE 0.017 0.002 PHE A1129 TRP 0.016 0.002 TRP B 241 HIS 0.006 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00585 (14359) covalent geometry : angle 0.64666 (19625) hydrogen bonds : bond 0.04682 ( 675) hydrogen bonds : angle 5.21061 ( 1894) *********************** 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 234 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6095 (ttt-90) cc_final: 0.5021 (ttp80) REVERT: A 193 ARG cc_start: 0.7216 (mtm180) cc_final: 0.5187 (mmp80) REVERT: A 232 ARG cc_start: 0.6222 (mtt180) cc_final: 0.5305 (mtm180) REVERT: A 263 GLU cc_start: 0.7467 (mp0) cc_final: 0.7006 (mp0) REVERT: A 459 MET cc_start: 0.8495 (tpp) cc_final: 0.7795 (tmm) REVERT: A 773 LYS cc_start: 0.7385 (mmmt) cc_final: 0.6535 (mppt) REVERT: A 793 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6238 (tt0) REVERT: A 1089 GLN cc_start: 0.7089 (mt0) cc_final: 0.6579 (mp10) REVERT: B 134 LYS cc_start: 0.7303 (ttpt) cc_final: 0.6083 (mmtm) REVERT: B 250 GLN cc_start: 0.7324 (mt0) cc_final: 0.6536 (mm-40) REVERT: B 325 ARG cc_start: 0.6208 (mtt90) cc_final: 0.5942 (mtm110) REVERT: C 236 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: C 249 ASN cc_start: 0.5658 (m-40) cc_final: 0.5414 (m110) REVERT: C 334 CYS cc_start: 0.6978 (m) cc_final: 0.6065 (t) REVERT: C 370 LYS cc_start: 0.8314 (mmtm) cc_final: 0.8041 (mttt) outliers start: 42 outliers final: 17 residues processed: 211 average time/residue: 0.7026 time to fit residues: 161.3041 Evaluate side-chains 189 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 1053 THR Chi-restraints excluded: chain A residue 1141 VAL 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 277 ASP Chi-restraints excluded: chain B residue 387 VAL 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 300 ILE Chi-restraints excluded: chain C residue 397 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 155 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.165551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127249 restraints weight = 14893.838| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.13 r_work: 0.3579 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14359 Z= 0.123 Angle : 0.520 10.274 19625 Z= 0.269 Chirality : 0.040 0.155 2101 Planarity : 0.005 0.050 2388 Dihedral : 13.762 86.069 2206 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.61 % Allowed : 12.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.21), residues: 1609 helix: 1.53 (0.20), residues: 703 sheet: 0.94 (0.31), residues: 247 loop : 0.13 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1071 TYR 0.020 0.002 TYR A1166 PHE 0.019 0.002 PHE A 539 TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00279 (14359) covalent geometry : angle 0.51982 (19625) hydrogen bonds : bond 0.03586 ( 675) hydrogen bonds : angle 4.83967 ( 1894) *********************** 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 215 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6048 (ttt-90) cc_final: 0.5051 (ttp80) REVERT: A 193 ARG cc_start: 0.7154 (mtm180) cc_final: 0.5260 (mmp80) REVERT: A 232 ARG cc_start: 0.6358 (mtt180) cc_final: 0.5556 (mtm180) REVERT: A 263 GLU cc_start: 0.7444 (mp0) cc_final: 0.7135 (mp0) REVERT: A 459 MET cc_start: 0.8539 (tpp) cc_final: 0.7909 (tmm) REVERT: A 773 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6583 (mppt) REVERT: A 776 ASP cc_start: 0.7955 (t0) cc_final: 0.7622 (t0) REVERT: A 1089 GLN cc_start: 0.7051 (mt0) cc_final: 0.6638 (mp10) REVERT: B 134 LYS cc_start: 0.7437 (ttpt) cc_final: 0.6229 (mmtt) REVERT: B 250 GLN cc_start: 0.7292 (mt0) cc_final: 0.6572 (mm-40) REVERT: B 308 ASP cc_start: 0.7479 (p0) cc_final: 0.7166 (p0) REVERT: B 325 ARG cc_start: 0.6252 (mtt90) cc_final: 0.5970 (mtm110) REVERT: C 183 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: C 236 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: C 249 ASN cc_start: 0.5815 (m-40) cc_final: 0.5608 (m110) REVERT: C 325 ARG cc_start: 0.5631 (mtm110) cc_final: 0.4881 (mmm160) REVERT: C 334 CYS cc_start: 0.6925 (m) cc_final: 0.6023 (t) REVERT: C 370 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8083 (mttt) outliers start: 37 outliers final: 15 residues processed: 197 average time/residue: 0.6957 time to fit residues: 149.3790 Evaluate side-chains 185 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 551 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1121 GLU 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 277 ASP 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 236 GLU Chi-restraints excluded: chain C residue 397 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 906 HIS A 922 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 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 = 0.3988 r_free = 0.3988 target = 0.162940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123964 restraints weight = 14924.733| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.15 r_work: 0.3553 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14359 Z= 0.177 Angle : 0.570 10.399 19625 Z= 0.292 Chirality : 0.042 0.162 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.791 83.993 2204 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.89 % Allowed : 13.11 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 1609 helix: 1.42 (0.20), residues: 702 sheet: 0.88 (0.31), residues: 241 loop : 0.07 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.020 0.002 PHE A 88 TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00418 (14359) covalent geometry : angle 0.56976 (19625) hydrogen bonds : bond 0.03943 ( 675) hydrogen bonds : angle 4.86805 ( 1894) *********************** 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 221 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6166 (ttt-90) cc_final: 0.5120 (ttp80) REVERT: A 193 ARG cc_start: 0.7263 (mtm180) cc_final: 0.5352 (mmp80) REVERT: A 263 GLU cc_start: 0.7475 (mp0) cc_final: 0.7058 (mp0) REVERT: A 459 MET cc_start: 0.8522 (tpp) cc_final: 0.7890 (tmm) REVERT: A 559 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5087 (mt) REVERT: A 776 ASP cc_start: 0.8075 (t0) cc_final: 0.7833 (t0) REVERT: A 793 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6399 (tt0) REVERT: A 922 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6141 (mt0) REVERT: A 1089 GLN cc_start: 0.7019 (mt0) cc_final: 0.6629 (mp10) REVERT: A 1164 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 124 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: B 134 LYS cc_start: 0.7435 (ttpt) cc_final: 0.6100 (mmtt) REVERT: B 250 GLN cc_start: 0.7293 (mt0) cc_final: 0.6611 (mm-40) REVERT: B 325 ARG cc_start: 0.6249 (mtt90) cc_final: 0.5888 (mtm110) REVERT: C 236 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: C 313 HIS cc_start: 0.5473 (t-90) cc_final: 0.4661 (m90) REVERT: C 325 ARG cc_start: 0.5701 (mtm110) cc_final: 0.4887 (mmm160) REVERT: C 334 CYS cc_start: 0.6920 (m) cc_final: 0.6019 (t) REVERT: C 370 LYS cc_start: 0.8381 (mmtm) cc_final: 0.8075 (mttt) outliers start: 41 outliers final: 18 residues processed: 206 average time/residue: 0.6942 time to fit residues: 155.7577 Evaluate side-chains 196 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 922 GLN Chi-restraints excluded: chain A residue 1164 PHE 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 277 ASP 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 236 GLU Chi-restraints excluded: chain C residue 397 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** A1102 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 = 0.4018 r_free = 0.4018 target = 0.165758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126999 restraints weight = 14820.788| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.15 r_work: 0.3589 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14359 Z= 0.115 Angle : 0.516 10.176 19625 Z= 0.264 Chirality : 0.039 0.165 2101 Planarity : 0.004 0.051 2388 Dihedral : 13.646 83.466 2203 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.33 % Allowed : 14.45 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.21), residues: 1609 helix: 1.67 (0.20), residues: 702 sheet: 1.02 (0.32), residues: 238 loop : 0.07 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.021 0.001 TYR A1166 PHE 0.020 0.001 PHE A 88 TRP 0.019 0.001 TRP B 241 HIS 0.004 0.001 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00263 (14359) covalent geometry : angle 0.51552 (19625) hydrogen bonds : bond 0.03286 ( 675) hydrogen bonds : angle 4.68543 ( 1894) *********************** 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 207 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6159 (ttt-90) cc_final: 0.5090 (ttp80) REVERT: A 193 ARG cc_start: 0.7179 (mtm180) cc_final: 0.5281 (mmp80) REVERT: A 263 GLU cc_start: 0.7410 (mp0) cc_final: 0.7012 (mp0) REVERT: A 459 MET cc_start: 0.8543 (tpp) cc_final: 0.7947 (tmm) REVERT: A 559 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5120 (mt) REVERT: A 922 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6152 (mt0) REVERT: A 1089 GLN cc_start: 0.7079 (mt0) cc_final: 0.6654 (mp10) REVERT: A 1164 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6474 (t80) REVERT: B 123 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: B 134 LYS cc_start: 0.7407 (ttpt) cc_final: 0.6088 (mmtt) REVERT: B 250 GLN cc_start: 0.7278 (mt0) cc_final: 0.6590 (mm-40) REVERT: B 308 ASP cc_start: 0.7552 (p0) cc_final: 0.7288 (p0) REVERT: B 325 ARG cc_start: 0.6283 (mtt90) cc_final: 0.5977 (mtm110) REVERT: B 450 ASN cc_start: 0.6608 (p0) cc_final: 0.6346 (p0) REVERT: B 465 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7447 (mpp) REVERT: C 89 ASP cc_start: 0.7207 (t0) cc_final: 0.6880 (m-30) REVERT: C 183 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: C 236 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: C 325 ARG cc_start: 0.5714 (mtm110) cc_final: 0.4836 (mmm160) REVERT: C 334 CYS cc_start: 0.6856 (m) cc_final: 0.5988 (t) REVERT: C 370 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8047 (mttt) outliers start: 33 outliers final: 16 residues processed: 191 average time/residue: 0.7166 time to fit residues: 148.8058 Evaluate side-chains 189 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 559 LEU 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 A residue 1164 PHE 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 371 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 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 = 0.3974 r_free = 0.3974 target = 0.161655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122589 restraints weight = 14903.455| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.15 r_work: 0.3539 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14359 Z= 0.219 Angle : 0.611 11.843 19625 Z= 0.311 Chirality : 0.044 0.162 2101 Planarity : 0.005 0.061 2388 Dihedral : 13.809 82.871 2203 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.96 % Allowed : 13.32 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1609 helix: 1.31 (0.19), residues: 704 sheet: 0.93 (0.32), residues: 224 loop : -0.01 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.023 0.002 PHE B 242 TRP 0.019 0.002 TRP B 241 HIS 0.006 0.001 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00527 (14359) covalent geometry : angle 0.61138 (19625) hydrogen bonds : bond 0.04183 ( 675) hydrogen bonds : angle 4.92720 ( 1894) *********************** 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 216 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6180 (ttt-90) cc_final: 0.5051 (ttp80) REVERT: A 193 ARG cc_start: 0.7228 (mtm180) cc_final: 0.5281 (mmp80) REVERT: A 263 GLU cc_start: 0.7415 (mp0) cc_final: 0.6979 (mp0) REVERT: A 459 MET cc_start: 0.8498 (tpp) cc_final: 0.7862 (tmm) REVERT: A 559 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5013 (mt) REVERT: A 922 GLN cc_start: 0.6478 (mp10) cc_final: 0.5984 (mt0) REVERT: A 1089 GLN cc_start: 0.7024 (mt0) cc_final: 0.6583 (mp10) REVERT: A 1112 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6664 (mtt) REVERT: A 1164 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6406 (t80) REVERT: B 134 LYS cc_start: 0.7443 (ttpt) cc_final: 0.6010 (mmtt) REVERT: B 250 GLN cc_start: 0.7256 (mt0) cc_final: 0.6488 (mm-40) REVERT: B 308 ASP cc_start: 0.7582 (p0) cc_final: 0.7235 (p0) REVERT: B 314 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6721 (ttp) REVERT: B 325 ARG cc_start: 0.6283 (mtt90) cc_final: 0.6058 (mtm110) REVERT: B 450 ASN cc_start: 0.6475 (p0) cc_final: 0.6190 (p0) REVERT: B 465 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: C 89 ASP cc_start: 0.7062 (t0) cc_final: 0.6735 (m-30) REVERT: C 236 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: C 313 HIS cc_start: 0.5436 (t-90) cc_final: 0.4609 (m90) REVERT: C 325 ARG cc_start: 0.5710 (mtm110) cc_final: 0.4900 (mmm160) REVERT: C 334 CYS cc_start: 0.6830 (m) cc_final: 0.5907 (t) REVERT: C 370 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8066 (mttt) REVERT: C 419 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7897 (tp30) outliers start: 42 outliers final: 22 residues processed: 199 average time/residue: 0.7275 time to fit residues: 157.2001 Evaluate side-chains 197 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 544 MET 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 910 MET Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE 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 314 MET 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 419 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 110 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** A1102 GLN ** 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 = 0.4008 r_free = 0.4008 target = 0.164821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125987 restraints weight = 14817.354| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.15 r_work: 0.3572 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14359 Z= 0.125 Angle : 0.528 11.746 19625 Z= 0.271 Chirality : 0.040 0.177 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.655 82.877 2203 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.68 % Allowed : 13.88 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.21), residues: 1609 helix: 1.60 (0.20), residues: 697 sheet: 1.00 (0.33), residues: 223 loop : 0.02 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.002 TYR A1166 PHE 0.026 0.002 PHE A1120 TRP 0.020 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00288 (14359) covalent geometry : angle 0.52810 (19625) hydrogen bonds : bond 0.03355 ( 675) hydrogen bonds : angle 4.70746 ( 1894) *********************** 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 213 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.546 Fit side-chains REVERT: A 177 ARG cc_start: 0.6189 (ttt-90) cc_final: 0.5126 (ttp80) REVERT: A 193 ARG cc_start: 0.7212 (mtm180) cc_final: 0.5308 (mmp80) REVERT: A 263 GLU cc_start: 0.7444 (mp0) cc_final: 0.7055 (mp0) REVERT: A 459 MET cc_start: 0.8474 (tpp) cc_final: 0.7891 (tmm) REVERT: A 559 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5122 (mt) REVERT: A 922 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.6060 (mt0) REVERT: A 1089 GLN cc_start: 0.7107 (mt0) cc_final: 0.6631 (mp10) REVERT: A 1164 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6501 (t80) REVERT: B 134 LYS cc_start: 0.7457 (ttpt) cc_final: 0.6080 (mmtt) REVERT: B 250 GLN cc_start: 0.7308 (mt0) cc_final: 0.6614 (mm-40) REVERT: B 308 ASP cc_start: 0.7498 (p0) cc_final: 0.7176 (p0) REVERT: B 325 ARG cc_start: 0.6311 (mtt90) cc_final: 0.6089 (mtm110) REVERT: B 465 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7435 (mpp) REVERT: C 89 ASP cc_start: 0.7175 (t0) cc_final: 0.6848 (m-30) REVERT: C 236 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: C 313 HIS cc_start: 0.5499 (t-90) cc_final: 0.4678 (m90) REVERT: C 325 ARG cc_start: 0.5725 (mtm110) cc_final: 0.4880 (mmm160) REVERT: C 334 CYS cc_start: 0.6809 (m) cc_final: 0.5914 (t) REVERT: C 370 LYS cc_start: 0.8393 (mmtm) cc_final: 0.8107 (mttt) outliers start: 38 outliers final: 13 residues processed: 196 average time/residue: 0.7084 time to fit residues: 151.0786 Evaluate side-chains 184 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 913 CYS Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 9 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** A1102 GLN ** 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 = 0.4012 r_free = 0.4012 target = 0.165049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126307 restraints weight = 14789.455| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.15 r_work: 0.3576 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14359 Z= 0.124 Angle : 0.537 13.008 19625 Z= 0.274 Chirality : 0.040 0.180 2101 Planarity : 0.005 0.051 2388 Dihedral : 13.592 82.808 2203 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.90 % Allowed : 15.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.21), residues: 1609 helix: 1.65 (0.20), residues: 697 sheet: 0.97 (0.33), residues: 216 loop : 0.03 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.002 TYR A1166 PHE 0.023 0.002 PHE A 273 TRP 0.020 0.001 TRP B 241 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00289 (14359) covalent geometry : angle 0.53735 (19625) hydrogen bonds : bond 0.03338 ( 675) hydrogen bonds : angle 4.68824 ( 1894) *********************** 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 196 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.547 Fit side-chains REVERT: A 177 ARG cc_start: 0.6150 (ttt-90) cc_final: 0.5077 (ttp80) REVERT: A 263 GLU cc_start: 0.7451 (mp0) cc_final: 0.7165 (mp0) REVERT: A 459 MET cc_start: 0.8475 (tpp) cc_final: 0.7884 (tmm) REVERT: A 558 LEU cc_start: 0.6576 (tm) cc_final: 0.6363 (tp) REVERT: A 559 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5101 (mt) REVERT: A 922 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6259 (mt0) REVERT: A 1089 GLN cc_start: 0.7101 (mt0) cc_final: 0.6610 (mp10) REVERT: A 1164 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6448 (t80) REVERT: B 134 LYS cc_start: 0.7439 (ttpt) cc_final: 0.6060 (mmtt) REVERT: B 250 GLN cc_start: 0.7294 (mt0) cc_final: 0.6576 (mm-40) REVERT: B 261 GLN cc_start: 0.7744 (pt0) cc_final: 0.7156 (mm110) REVERT: B 308 ASP cc_start: 0.7470 (p0) cc_final: 0.7098 (p0) REVERT: B 314 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7011 (ttp) REVERT: B 325 ARG cc_start: 0.6285 (mtt90) cc_final: 0.6049 (mtm110) REVERT: B 465 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7370 (mpp) REVERT: C 89 ASP cc_start: 0.7222 (t0) cc_final: 0.6904 (m-30) REVERT: C 236 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: C 325 ARG cc_start: 0.5737 (mtm110) cc_final: 0.4857 (mmm160) REVERT: C 334 CYS cc_start: 0.6775 (m) cc_final: 0.5867 (t) REVERT: C 370 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8090 (mttt) outliers start: 27 outliers final: 13 residues processed: 183 average time/residue: 0.7137 time to fit residues: 142.1024 Evaluate side-chains 183 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 913 CYS Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 314 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** A1102 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 = 0.4010 r_free = 0.4010 target = 0.164897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126111 restraints weight = 14926.380| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.15 r_work: 0.3577 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14359 Z= 0.132 Angle : 0.538 12.526 19625 Z= 0.275 Chirality : 0.040 0.163 2101 Planarity : 0.005 0.051 2388 Dihedral : 13.571 82.561 2203 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.04 % Allowed : 15.36 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.21), residues: 1609 helix: 1.65 (0.20), residues: 697 sheet: 0.97 (0.33), residues: 216 loop : 0.04 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1071 TYR 0.022 0.002 TYR A1166 PHE 0.024 0.002 PHE B 242 TRP 0.021 0.001 TRP B 241 HIS 0.004 0.001 HIS A 911 Details of bonding type rmsd covalent geometry : bond 0.00308 (14359) covalent geometry : angle 0.53755 (19625) hydrogen bonds : bond 0.03389 ( 675) hydrogen bonds : angle 4.69099 ( 1894) *********************** 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 201 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.573 Fit side-chains REVERT: A 177 ARG cc_start: 0.6166 (ttt-90) cc_final: 0.5150 (ttp80) REVERT: A 263 GLU cc_start: 0.7461 (mp0) cc_final: 0.7178 (mp0) REVERT: A 459 MET cc_start: 0.8485 (tpp) cc_final: 0.7906 (tmm) REVERT: A 558 LEU cc_start: 0.6600 (tm) cc_final: 0.6363 (tp) REVERT: A 559 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5096 (mt) REVERT: A 1089 GLN cc_start: 0.7105 (mt0) cc_final: 0.6667 (mp10) REVERT: A 1164 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6447 (t80) REVERT: B 123 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: B 134 LYS cc_start: 0.7419 (ttpt) cc_final: 0.6040 (mmtt) REVERT: B 250 GLN cc_start: 0.7321 (mt0) cc_final: 0.6577 (mm-40) REVERT: B 308 ASP cc_start: 0.7545 (p0) cc_final: 0.7193 (p0) REVERT: B 314 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6979 (ttp) REVERT: B 325 ARG cc_start: 0.6248 (mtt90) cc_final: 0.6013 (mtm110) REVERT: B 465 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7379 (mpp) REVERT: C 89 ASP cc_start: 0.7216 (t0) cc_final: 0.6904 (m-30) REVERT: C 236 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: C 325 ARG cc_start: 0.5698 (mtm110) cc_final: 0.4814 (mmm160) REVERT: C 334 CYS cc_start: 0.6792 (m) cc_final: 0.5886 (t) REVERT: C 370 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8101 (mttt) outliers start: 29 outliers final: 11 residues processed: 187 average time/residue: 0.7049 time to fit residues: 143.3360 Evaluate side-chains 180 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 913 CYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 314 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 95 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** ** A1102 GLN ** 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 = 0.3993 r_free = 0.3993 target = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124530 restraints weight = 14903.786| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.14 r_work: 0.3556 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14359 Z= 0.164 Angle : 0.581 12.438 19625 Z= 0.295 Chirality : 0.041 0.159 2101 Planarity : 0.005 0.051 2388 Dihedral : 13.620 82.170 2203 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.76 % Allowed : 15.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.20), residues: 1609 helix: 1.50 (0.20), residues: 698 sheet: 0.99 (0.33), residues: 223 loop : 0.02 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.027 0.002 PHE B 242 TRP 0.024 0.001 TRP B 241 HIS 0.004 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00388 (14359) covalent geometry : angle 0.58058 (19625) hydrogen bonds : bond 0.03742 ( 675) hydrogen bonds : angle 4.80170 ( 1894) ********************** 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 192 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.540 Fit side-chains REVERT: A 177 ARG cc_start: 0.6216 (ttt-90) cc_final: 0.5134 (ttp80) REVERT: A 263 GLU cc_start: 0.7472 (mp0) cc_final: 0.7193 (mp0) REVERT: A 454 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: A 459 MET cc_start: 0.8502 (tpp) cc_final: 0.7928 (tmm) REVERT: A 558 LEU cc_start: 0.6629 (tm) cc_final: 0.6345 (tp) REVERT: A 559 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5042 (mt) REVERT: A 1089 GLN cc_start: 0.7131 (mt0) cc_final: 0.6689 (mp10) REVERT: A 1164 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6482 (t80) REVERT: B 134 LYS cc_start: 0.7440 (ttpt) cc_final: 0.6022 (mmtt) REVERT: B 250 GLN cc_start: 0.7315 (mt0) cc_final: 0.6572 (mm-40) REVERT: B 261 GLN cc_start: 0.7842 (pt0) cc_final: 0.7249 (mm110) REVERT: B 308 ASP cc_start: 0.7615 (p0) cc_final: 0.7219 (p0) REVERT: B 314 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6921 (ttp) REVERT: B 325 ARG cc_start: 0.6248 (mtt90) cc_final: 0.5980 (mtp180) REVERT: B 465 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7317 (mpp) REVERT: C 89 ASP cc_start: 0.7157 (t0) cc_final: 0.6846 (m-30) REVERT: C 129 ASP cc_start: 0.6165 (t70) cc_final: 0.5704 (t70) REVERT: C 236 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: C 325 ARG cc_start: 0.5649 (mtm110) cc_final: 0.4770 (mmm160) REVERT: C 334 CYS cc_start: 0.6787 (m) cc_final: 0.5853 (t) REVERT: C 370 LYS cc_start: 0.8371 (mmtm) cc_final: 0.8090 (mttt) outliers start: 25 outliers final: 12 residues processed: 182 average time/residue: 0.7044 time to fit residues: 139.5714 Evaluate side-chains 182 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 1164 PHE 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 314 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 261 GLN B 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127371 restraints weight = 14867.402| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.16 r_work: 0.3590 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14359 Z= 0.119 Angle : 0.538 11.887 19625 Z= 0.275 Chirality : 0.040 0.171 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.546 82.159 2203 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.48 % Allowed : 16.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.21), residues: 1609 helix: 1.67 (0.20), residues: 698 sheet: 0.97 (0.33), residues: 216 loop : 0.11 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.026 0.002 PHE A 273 TRP 0.037 0.001 TRP A 918 HIS 0.003 0.001 HIS A 911 Details of bonding type rmsd covalent geometry : bond 0.00275 (14359) covalent geometry : angle 0.53753 (19625) hydrogen bonds : bond 0.03329 ( 675) hydrogen bonds : angle 4.68034 ( 1894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6072.40 seconds wall clock time: 104 minutes 13.02 seconds (6253.02 seconds total)