Starting phenix.real_space_refine on Fri Feb 14 17:23:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7shk_25127/02_2025/7shk_25127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7shk_25127/02_2025/7shk_25127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7shk_25127/02_2025/7shk_25127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7shk_25127/02_2025/7shk_25127.map" model { file = "/net/cci-nas-00/data/ceres_data/7shk_25127/02_2025/7shk_25127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7shk_25127/02_2025/7shk_25127.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 82 5.16 5 C 6689 2.51 5 N 1761 2.21 5 O 1949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10485 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 6100 Classifications: {'peptide': 744} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 723} Chain: "B" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2228 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264} Chain: "R" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9419 SG CYS L 356 45.915 26.856 135.856 1.00 90.44 S ATOM 9433 SG CYS L 358 47.271 23.972 137.907 1.00 94.83 S ATOM 9746 SG CYS L 400 49.660 26.302 136.190 1.00 90.30 S ATOM 9773 SG CYS L 404 47.414 23.969 134.046 1.00 93.77 S ATOM 10111 SG CYS R 53 41.482 36.616 58.649 1.00265.35 S ATOM 10131 SG CYS R 56 43.220 33.958 60.783 1.00263.20 S ATOM 10157 SG CYS R 68 42.592 33.335 57.039 1.00270.24 S ATOM 10043 SG CYS R 42 37.367 38.588 51.529 1.00257.20 S ATOM 10062 SG CYS R 45 39.843 39.804 53.987 1.00256.03 S ATOM 10275 SG CYS R 83 38.002 37.462 55.913 1.00272.17 S ATOM 10207 SG CYS R 75 30.111 32.093 44.690 1.00279.86 S ATOM 10367 SG CYS R 94 28.909 35.299 46.659 1.00288.30 S Time building chain proxies: 6.19, per 1000 atoms: 0.59 Number of scatterers: 10485 At special positions: 0 Unit cell: (113.025, 101.475, 177.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 82 16.00 O 1949 8.00 N 1761 7.00 C 6689 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: 2.42 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 356 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 358 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 400 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 404 " pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 68 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " Number of angles added : 12 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2518 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 53.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.685A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.709A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.694A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.680A pdb=" N ILE A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.740A pdb=" N ILE A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 200 through 208 Processing helix chain 'A' and resid 208 through 230 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.803A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.623A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.948A pdb=" N ALA A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 4.666A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 357 Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.704A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 3.879A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.972A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 497 removed outlier: 4.180A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 548 removed outlier: 4.552A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.910A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.792A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.704A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.698A pdb=" N ASP B 41 " --> pdb=" O PRO B 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 removed outlier: 4.087A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'L' and resid 169 through 174 removed outlier: 3.888A pdb=" N LEU L 174 " --> pdb=" O MET L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 219 removed outlier: 3.613A pdb=" N CYS L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER L 219 " --> pdb=" O VAL L 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 214 through 219' Processing helix chain 'L' and resid 220 through 225 removed outlier: 3.776A pdb=" N ARG L 223 " --> pdb=" O THR L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 246 Processing helix chain 'L' and resid 263 through 269 removed outlier: 4.339A pdb=" N GLY L 267 " --> pdb=" O PHE L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 292 removed outlier: 3.685A pdb=" N LYS L 290 " --> pdb=" O ASN L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 333 Processing helix chain 'L' and resid 343 through 352 removed outlier: 3.516A pdb=" N SER L 351 " --> pdb=" O CYS L 347 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU L 352 " --> pdb=" O GLN L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 415 removed outlier: 3.603A pdb=" N SER L 406 " --> pdb=" O LEU L 402 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN L 407 " --> pdb=" O THR L 403 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE L 408 " --> pdb=" O CYS L 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 89 removed outlier: 3.512A pdb=" N LYS R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 513 removed outlier: 6.108A pdb=" N SER A 506 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA R 29 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN A 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA R 31 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR A 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP R 33 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TRP R 35 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 513 removed outlier: 6.108A pdb=" N SER A 506 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA R 29 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN A 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA R 31 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR A 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP R 33 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TRP R 35 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL R 24 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LYS A 565 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS R 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 695 removed outlier: 4.158A pdb=" N LEU A 694 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 741 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.635A pdb=" N ALA B 73 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 13 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LYS C 32 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N PHE B 15 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL C 60 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 20 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 135 through 138 removed outlier: 6.604A pdb=" N LEU L 136 " --> pdb=" O GLN L 158 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER L 160 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE L 138 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU L 180 " --> pdb=" O ILE L 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP L 230 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU L 229 " --> pdb=" O LYS L 253 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU L 275 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU L 295 " --> pdb=" O THR L 381 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL L 383 " --> pdb=" O GLU L 295 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU L 297 " --> pdb=" O VAL L 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 313 through 314 removed outlier: 3.617A pdb=" N ASP L 313 " --> pdb=" O GLN L 368 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN L 368 " --> pdb=" O ASP L 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 354 through 355 removed outlier: 3.807A pdb=" N LYS L 354 " --> pdb=" O CYS L 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 78 through 80 Processing sheet with id=AB2, first strand: chain 'R' and resid 93 through 94 507 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1739 1.30 - 1.43: 2669 1.43 - 1.55: 6158 1.55 - 1.68: 4 1.68 - 1.81: 125 Bond restraints: 10695 Sorted by residual: bond pdb=" C LEU L 322 " pdb=" O LEU L 322 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.17e-02 7.31e+03 3.60e+01 bond pdb=" C PRO L 343 " pdb=" O PRO L 343 " ideal model delta sigma weight residual 1.233 1.167 0.066 1.19e-02 7.06e+03 3.04e+01 bond pdb=" C PRO L 321 " pdb=" O PRO L 321 " ideal model delta sigma weight residual 1.233 1.175 0.058 1.19e-02 7.06e+03 2.37e+01 bond pdb=" N PRO L 321 " pdb=" CA PRO L 321 " ideal model delta sigma weight residual 1.466 1.413 0.053 1.24e-02 6.50e+03 1.84e+01 bond pdb=" N THR L 325 " pdb=" CA THR L 325 " ideal model delta sigma weight residual 1.459 1.512 -0.053 1.23e-02 6.61e+03 1.83e+01 ... (remaining 10690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13969 1.94 - 3.89: 343 3.89 - 5.83: 101 5.83 - 7.78: 28 7.78 - 9.72: 14 Bond angle restraints: 14455 Sorted by residual: angle pdb=" N ALA L 326 " pdb=" CA ALA L 326 " pdb=" C ALA L 326 " ideal model delta sigma weight residual 111.36 102.85 8.51 1.09e+00 8.42e-01 6.10e+01 angle pdb=" N ARG L 328 " pdb=" CA ARG L 328 " pdb=" C ARG L 328 " ideal model delta sigma weight residual 111.71 103.69 8.02 1.15e+00 7.56e-01 4.86e+01 angle pdb=" N MET C 105 " pdb=" CA MET C 105 " pdb=" C MET C 105 " ideal model delta sigma weight residual 111.28 104.00 7.28 1.09e+00 8.42e-01 4.46e+01 angle pdb=" N GLU C 102 " pdb=" CA GLU C 102 " pdb=" C GLU C 102 " ideal model delta sigma weight residual 111.28 104.40 6.88 1.09e+00 8.42e-01 3.98e+01 angle pdb=" C THR L 345 " pdb=" CA THR L 345 " pdb=" CB THR L 345 " ideal model delta sigma weight residual 110.88 101.16 9.72 1.57e+00 4.06e-01 3.84e+01 ... (remaining 14450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5873 17.99 - 35.98: 554 35.98 - 53.97: 98 53.97 - 71.96: 17 71.96 - 89.96: 4 Dihedral angle restraints: 6546 sinusoidal: 2683 harmonic: 3863 Sorted by residual: dihedral pdb=" CA MET A 605 " pdb=" C MET A 605 " pdb=" N ASN A 606 " pdb=" CA ASN A 606 " ideal model delta harmonic sigma weight residual 180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" C TYR L 337 " pdb=" N TYR L 337 " pdb=" CA TYR L 337 " pdb=" CB TYR L 337 " ideal model delta harmonic sigma weight residual -122.60 -110.54 -12.06 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C THR L 345 " pdb=" N THR L 345 " pdb=" CA THR L 345 " pdb=" CB THR L 345 " ideal model delta harmonic sigma weight residual -122.00 -110.67 -11.33 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 6543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1351 0.056 - 0.112: 234 0.112 - 0.168: 32 0.168 - 0.225: 6 0.225 - 0.281: 8 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CB VAL A 665 " pdb=" CA VAL A 665 " pdb=" CG1 VAL A 665 " pdb=" CG2 VAL A 665 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR L 337 " pdb=" N TYR L 337 " pdb=" C TYR L 337 " pdb=" CB TYR L 337 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE L 335 " pdb=" N ILE L 335 " pdb=" C ILE L 335 " pdb=" CB ILE L 335 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1628 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 68 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 69 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 348 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLN L 348 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN L 348 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP L 349 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 104 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU C 104 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU C 104 " 0.020 2.00e-02 2.50e+03 pdb=" N MET C 105 " 0.018 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 895 2.74 - 3.28: 11163 3.28 - 3.82: 17362 3.82 - 4.36: 20504 4.36 - 4.90: 34403 Nonbonded interactions: 84327 Sorted by model distance: nonbonded pdb=" OH TYR A 298 " pdb=" OD2 ASP A 361 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR A 407 " pdb=" OE1 GLU A 410 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASN L 287 " pdb=" NZ LYS L 290 " model vdw 2.244 3.120 nonbonded pdb=" O VAL A 184 " pdb=" OG SER A 187 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP A 396 " pdb=" NH1 ARG A 442 " model vdw 2.269 3.120 ... (remaining 84322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.005 0.107 10695 Z= 0.326 Angle : 0.819 9.725 14455 Z= 0.495 Chirality : 0.047 0.281 1631 Planarity : 0.006 0.109 1838 Dihedral : 14.182 89.956 4028 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.25 % Allowed : 0.68 % Favored : 99.07 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1285 helix: 0.62 (0.21), residues: 603 sheet: -0.44 (0.63), residues: 77 loop : -0.86 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.005 0.001 HIS B 9 PHE 0.012 0.001 PHE A 588 TYR 0.017 0.002 TYR A 596 ARG 0.009 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 222 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.7597 (tpp) cc_final: 0.7177 (tpp) REVERT: A 335 MET cc_start: 0.7706 (mmm) cc_final: 0.7499 (mpp) REVERT: A 389 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7776 (tp30) REVERT: A 685 VAL cc_start: 0.9207 (t) cc_final: 0.8996 (t) REVERT: B 41 ASP cc_start: 0.6578 (m-30) cc_final: 0.6377 (m-30) REVERT: C 111 ASP cc_start: 0.6928 (t0) cc_final: 0.6638 (m-30) REVERT: L 247 LYS cc_start: 0.8124 (mptt) cc_final: 0.7634 (ttpt) REVERT: L 261 GLN cc_start: 0.7309 (pm20) cc_final: 0.6740 (pt0) REVERT: R 26 LYS cc_start: 0.8325 (tptt) cc_final: 0.8112 (tptt) REVERT: R 35 TRP cc_start: 0.6788 (m100) cc_final: 0.5865 (m-10) REVERT: R 77 HIS cc_start: 0.4665 (m170) cc_final: 0.4416 (m170) REVERT: R 87 TRP cc_start: 0.7785 (t-100) cc_final: 0.7516 (t-100) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 0.2561 time to fit residues: 78.7125 Evaluate side-chains 174 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 324 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.0170 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN C 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.128607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.099728 restraints weight = 21696.371| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.28 r_work: 0.3647 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10695 Z= 0.260 Angle : 0.654 7.844 14455 Z= 0.337 Chirality : 0.043 0.163 1631 Planarity : 0.005 0.074 1838 Dihedral : 4.839 60.525 1404 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.12 % Allowed : 8.58 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1285 helix: 0.84 (0.21), residues: 615 sheet: -0.68 (0.58), residues: 90 loop : -0.87 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 35 HIS 0.004 0.001 HIS A 547 PHE 0.023 0.002 PHE L 300 TYR 0.016 0.001 TYR A 596 ARG 0.006 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6804 (mp0) REVERT: A 389 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7912 (tp30) REVERT: A 480 MET cc_start: 0.7502 (tmm) cc_final: 0.7041 (tmm) REVERT: A 688 MET cc_start: 0.8807 (tmm) cc_final: 0.8270 (tmm) REVERT: A 689 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8805 (mmmt) REVERT: A 699 LEU cc_start: 0.9456 (mt) cc_final: 0.9211 (mm) REVERT: B 45 TYR cc_start: 0.8281 (m-80) cc_final: 0.7761 (m-80) REVERT: C 111 ASP cc_start: 0.7909 (t0) cc_final: 0.7374 (m-30) REVERT: L 247 LYS cc_start: 0.8092 (mptt) cc_final: 0.7539 (ttpt) REVERT: L 334 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7954 (mtp85) REVERT: R 26 LYS cc_start: 0.8300 (tptt) cc_final: 0.8089 (tptt) REVERT: R 77 HIS cc_start: 0.4805 (m170) cc_final: 0.4540 (m170) REVERT: R 87 TRP cc_start: 0.7630 (t-100) cc_final: 0.7381 (t-100) outliers start: 25 outliers final: 15 residues processed: 199 average time/residue: 0.2221 time to fit residues: 63.7734 Evaluate side-chains 185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 362 CYS Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain L residue 403 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN A 547 HIS ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.130766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.102168 restraints weight = 21791.153| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.31 r_work: 0.3690 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10695 Z= 0.185 Angle : 0.606 7.976 14455 Z= 0.308 Chirality : 0.041 0.245 1631 Planarity : 0.004 0.062 1838 Dihedral : 4.305 25.945 1401 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.70 % Allowed : 11.89 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1285 helix: 0.97 (0.21), residues: 620 sheet: -0.59 (0.56), residues: 96 loop : -0.68 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.005 0.001 HIS L 156 PHE 0.025 0.001 PHE A 543 TYR 0.015 0.001 TYR L 337 ARG 0.007 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 10 PHE cc_start: 0.7189 (t80) cc_final: 0.6932 (t80) REVERT: A 138 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6674 (mp0) REVERT: A 297 MET cc_start: 0.8576 (tpp) cc_final: 0.7849 (tpp) REVERT: A 389 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7946 (tp30) REVERT: A 476 MET cc_start: 0.7312 (ttm) cc_final: 0.6959 (ttm) REVERT: B 32 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7716 (pp20) REVERT: B 45 TYR cc_start: 0.8222 (m-80) cc_final: 0.7808 (m-80) REVERT: C 111 ASP cc_start: 0.7838 (t0) cc_final: 0.7348 (m-30) REVERT: L 334 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.8108 (mtp85) REVERT: R 26 LYS cc_start: 0.8304 (tptt) cc_final: 0.8070 (tptt) REVERT: R 77 HIS cc_start: 0.4617 (m170) cc_final: 0.4317 (m170) REVERT: R 87 TRP cc_start: 0.7570 (t-100) cc_final: 0.7346 (t-100) outliers start: 20 outliers final: 12 residues processed: 199 average time/residue: 0.2338 time to fit residues: 66.2277 Evaluate side-chains 187 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.130528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.101720 restraints weight = 21737.952| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.33 r_work: 0.3691 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10695 Z= 0.190 Angle : 0.594 7.810 14455 Z= 0.304 Chirality : 0.041 0.161 1631 Planarity : 0.004 0.056 1838 Dihedral : 4.260 25.632 1401 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.70 % Allowed : 13.25 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1285 helix: 1.05 (0.21), residues: 618 sheet: -0.59 (0.56), residues: 96 loop : -0.66 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.014 0.001 HIS B 10 PHE 0.022 0.001 PHE A 543 TYR 0.017 0.001 TYR L 337 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6666 (mp0) REVERT: A 197 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7489 (mmmt) REVERT: A 297 MET cc_start: 0.8568 (tpp) cc_final: 0.7857 (tpp) REVERT: A 389 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7960 (tp30) REVERT: A 451 MET cc_start: 0.8414 (tpp) cc_final: 0.8038 (tpp) REVERT: B 32 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7793 (pp20) REVERT: B 45 TYR cc_start: 0.8209 (m-80) cc_final: 0.7771 (m-80) REVERT: C 111 ASP cc_start: 0.7811 (t0) cc_final: 0.7343 (m-30) REVERT: L 247 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7469 (ttpt) REVERT: L 334 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8210 (mtp85) REVERT: L 352 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6747 (pp) REVERT: R 77 HIS cc_start: 0.4657 (m170) cc_final: 0.4354 (m170) REVERT: R 87 TRP cc_start: 0.7556 (t-100) cc_final: 0.7351 (t-100) outliers start: 20 outliers final: 15 residues processed: 199 average time/residue: 0.2265 time to fit residues: 64.6678 Evaluate side-chains 192 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 125 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.129955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.100927 restraints weight = 21728.181| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.33 r_work: 0.3679 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.204 Angle : 0.601 8.486 14455 Z= 0.308 Chirality : 0.041 0.164 1631 Planarity : 0.004 0.054 1838 Dihedral : 4.261 25.997 1401 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.04 % Allowed : 14.36 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1285 helix: 1.11 (0.21), residues: 614 sheet: -0.74 (0.56), residues: 98 loop : -0.57 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.006 0.001 HIS B 10 PHE 0.019 0.001 PHE A 543 TYR 0.017 0.001 TYR L 337 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6740 (mp0) REVERT: A 197 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7491 (mmmt) REVERT: A 389 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7991 (tp30) REVERT: A 535 LYS cc_start: 0.9285 (tppp) cc_final: 0.8899 (tppt) REVERT: A 539 MET cc_start: 0.8793 (mmm) cc_final: 0.8237 (mmm) REVERT: A 725 LEU cc_start: 0.9378 (mm) cc_final: 0.8891 (mm) REVERT: B 32 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7811 (pp20) REVERT: B 42 GLN cc_start: 0.8427 (pm20) cc_final: 0.8045 (pm20) REVERT: B 45 TYR cc_start: 0.8294 (m-80) cc_final: 0.7820 (m-80) REVERT: B 87 GLU cc_start: 0.7969 (pt0) cc_final: 0.7762 (pt0) REVERT: C 111 ASP cc_start: 0.7812 (t0) cc_final: 0.7321 (m-30) REVERT: L 247 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7479 (ttpt) REVERT: L 261 GLN cc_start: 0.7795 (pm20) cc_final: 0.7535 (pm20) REVERT: L 334 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8234 (mtp85) REVERT: L 352 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6686 (pp) REVERT: R 26 LYS cc_start: 0.8264 (tptt) cc_final: 0.8016 (tptt) REVERT: R 77 HIS cc_start: 0.4628 (m170) cc_final: 0.4331 (m170) REVERT: R 87 TRP cc_start: 0.7603 (t-100) cc_final: 0.7396 (t-100) outliers start: 24 outliers final: 17 residues processed: 201 average time/residue: 0.2235 time to fit residues: 64.5838 Evaluate side-chains 195 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.130996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.103011 restraints weight = 22042.625| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.22 r_work: 0.3703 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.184 Angle : 0.612 9.807 14455 Z= 0.310 Chirality : 0.041 0.185 1631 Planarity : 0.004 0.051 1838 Dihedral : 4.217 26.507 1401 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 14.87 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1285 helix: 1.11 (0.21), residues: 614 sheet: -0.66 (0.56), residues: 96 loop : -0.57 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.006 0.001 HIS B 10 PHE 0.021 0.001 PHE A 548 TYR 0.018 0.001 TYR L 337 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6669 (mp0) REVERT: A 197 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7455 (mmmt) REVERT: A 389 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8009 (tp30) REVERT: A 451 MET cc_start: 0.8567 (tpp) cc_final: 0.8331 (tpp) REVERT: A 535 LYS cc_start: 0.9274 (tppp) cc_final: 0.8855 (tppt) REVERT: A 539 MET cc_start: 0.8807 (mmm) cc_final: 0.8254 (mmm) REVERT: B 32 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7817 (pp20) REVERT: B 42 GLN cc_start: 0.8352 (pm20) cc_final: 0.7939 (pm20) REVERT: B 45 TYR cc_start: 0.8312 (m-80) cc_final: 0.7829 (m-80) REVERT: C 111 ASP cc_start: 0.7746 (t0) cc_final: 0.7285 (m-30) REVERT: L 247 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7444 (ttpt) REVERT: L 261 GLN cc_start: 0.7808 (pm20) cc_final: 0.7580 (pm20) REVERT: L 295 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6278 (mp0) REVERT: L 352 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6748 (pp) REVERT: R 26 LYS cc_start: 0.8231 (tptt) cc_final: 0.8008 (tptt) REVERT: R 77 HIS cc_start: 0.4649 (m170) cc_final: 0.4350 (m170) REVERT: R 87 TRP cc_start: 0.7634 (t-100) cc_final: 0.7427 (t-100) outliers start: 24 outliers final: 18 residues processed: 197 average time/residue: 0.2215 time to fit residues: 62.7614 Evaluate side-chains 195 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 0.0370 chunk 93 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.130879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.102701 restraints weight = 22193.055| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.24 r_work: 0.3697 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10695 Z= 0.194 Angle : 0.631 10.233 14455 Z= 0.319 Chirality : 0.041 0.186 1631 Planarity : 0.004 0.050 1838 Dihedral : 4.213 26.721 1401 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.04 % Allowed : 16.48 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1285 helix: 1.12 (0.21), residues: 612 sheet: -0.63 (0.60), residues: 86 loop : -0.56 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 35 HIS 0.005 0.001 HIS L 156 PHE 0.021 0.001 PHE A 548 TYR 0.019 0.001 TYR L 337 ARG 0.010 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6682 (mp0) REVERT: A 197 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7464 (mmmt) REVERT: A 389 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7987 (tp30) REVERT: A 451 MET cc_start: 0.8610 (tpp) cc_final: 0.8354 (tpp) REVERT: A 605 MET cc_start: 0.8233 (ppp) cc_final: 0.7667 (ppp) REVERT: B 32 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7838 (pp20) REVERT: B 42 GLN cc_start: 0.8310 (pm20) cc_final: 0.7837 (pm20) REVERT: B 45 TYR cc_start: 0.8325 (m-80) cc_final: 0.7841 (m-80) REVERT: C 111 ASP cc_start: 0.7748 (t0) cc_final: 0.7245 (m-30) REVERT: L 247 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7418 (ttpt) REVERT: L 261 GLN cc_start: 0.7882 (pm20) cc_final: 0.7568 (pm20) REVERT: L 352 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6702 (pp) REVERT: R 26 LYS cc_start: 0.8235 (tptt) cc_final: 0.7960 (tptt) REVERT: R 77 HIS cc_start: 0.4780 (m170) cc_final: 0.4469 (m170) REVERT: R 87 TRP cc_start: 0.7643 (t-100) cc_final: 0.7441 (t-100) outliers start: 24 outliers final: 21 residues processed: 191 average time/residue: 0.2295 time to fit residues: 62.9427 Evaluate side-chains 191 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.127001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.097409 restraints weight = 21570.158| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.36 r_work: 0.3657 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10695 Z= 0.233 Angle : 0.653 11.192 14455 Z= 0.329 Chirality : 0.042 0.183 1631 Planarity : 0.005 0.071 1838 Dihedral : 4.254 25.790 1401 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.38 % Allowed : 16.48 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1285 helix: 1.04 (0.21), residues: 613 sheet: -0.72 (0.57), residues: 96 loop : -0.58 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 72 HIS 0.004 0.001 HIS L 156 PHE 0.017 0.001 PHE A 543 TYR 0.018 0.001 TYR L 337 ARG 0.014 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6874 (mp0) REVERT: A 197 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7475 (mmmt) REVERT: A 335 MET cc_start: 0.8149 (mpp) cc_final: 0.7906 (mpp) REVERT: A 389 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7974 (tp30) REVERT: A 451 MET cc_start: 0.8599 (tpp) cc_final: 0.8321 (tpp) REVERT: A 535 LYS cc_start: 0.9302 (tppp) cc_final: 0.8986 (tppt) REVERT: A 566 MET cc_start: 0.6003 (mmm) cc_final: 0.4516 (tpt) REVERT: A 605 MET cc_start: 0.8281 (ppp) cc_final: 0.7734 (ppp) REVERT: A 666 GLU cc_start: 0.9141 (tp30) cc_final: 0.8883 (mt-10) REVERT: A 699 LEU cc_start: 0.9426 (mt) cc_final: 0.9218 (mm) REVERT: A 717 MET cc_start: 0.9034 (mtp) cc_final: 0.8549 (ptp) REVERT: B 32 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7927 (pp20) REVERT: B 42 GLN cc_start: 0.8345 (pm20) cc_final: 0.7839 (pm20) REVERT: B 45 TYR cc_start: 0.8320 (m-80) cc_final: 0.7823 (m-80) REVERT: C 111 ASP cc_start: 0.7799 (t0) cc_final: 0.7265 (m-30) REVERT: L 247 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7419 (ttpt) REVERT: L 261 GLN cc_start: 0.7804 (pm20) cc_final: 0.7407 (pm20) REVERT: L 295 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6269 (mp0) REVERT: L 352 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6642 (pp) REVERT: R 77 HIS cc_start: 0.4879 (m170) cc_final: 0.4560 (m170) outliers start: 28 outliers final: 25 residues processed: 192 average time/residue: 0.2202 time to fit residues: 61.1650 Evaluate side-chains 199 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 362 CYS Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.125964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.096178 restraints weight = 21821.879| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.38 r_work: 0.3640 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10695 Z= 0.250 Angle : 0.670 10.993 14455 Z= 0.339 Chirality : 0.043 0.190 1631 Planarity : 0.004 0.047 1838 Dihedral : 4.377 26.862 1401 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.21 % Allowed : 16.99 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1285 helix: 0.93 (0.21), residues: 616 sheet: -0.73 (0.58), residues: 96 loop : -0.62 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 87 HIS 0.005 0.001 HIS B 9 PHE 0.017 0.002 PHE A 548 TYR 0.019 0.001 TYR L 337 ARG 0.004 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7228 (mm-30) cc_final: 0.7007 (mp0) REVERT: A 335 MET cc_start: 0.8170 (mpp) cc_final: 0.7928 (mpp) REVERT: A 389 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7991 (tp30) REVERT: A 451 MET cc_start: 0.8622 (tpp) cc_final: 0.8359 (tpp) REVERT: A 535 LYS cc_start: 0.9267 (tppp) cc_final: 0.8932 (tppt) REVERT: A 566 MET cc_start: 0.6064 (mmm) cc_final: 0.4271 (tpp) REVERT: A 605 MET cc_start: 0.8204 (ppp) cc_final: 0.7710 (ppp) REVERT: A 699 LEU cc_start: 0.9431 (mt) cc_final: 0.9217 (mm) REVERT: A 717 MET cc_start: 0.9037 (mtp) cc_final: 0.8533 (ptp) REVERT: B 42 GLN cc_start: 0.8331 (pm20) cc_final: 0.7797 (pm20) REVERT: C 111 ASP cc_start: 0.7811 (t0) cc_final: 0.7252 (m-30) REVERT: L 181 ASP cc_start: 0.6845 (m-30) cc_final: 0.6308 (t0) REVERT: L 204 ILE cc_start: 0.7328 (mt) cc_final: 0.6841 (mt) REVERT: L 247 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7477 (ttpt) REVERT: L 261 GLN cc_start: 0.7843 (pm20) cc_final: 0.7376 (pm20) REVERT: L 295 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6327 (mp0) REVERT: L 352 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6650 (pp) REVERT: R 77 HIS cc_start: 0.4685 (m170) cc_final: 0.4426 (m170) outliers start: 26 outliers final: 24 residues processed: 188 average time/residue: 0.2216 time to fit residues: 60.0252 Evaluate side-chains 193 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 146 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 401 SER Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 0.0040 overall best weight: 0.7532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.129683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.100478 restraints weight = 21741.808| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.34 r_work: 0.3674 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10695 Z= 0.209 Angle : 0.656 11.263 14455 Z= 0.331 Chirality : 0.042 0.181 1631 Planarity : 0.004 0.048 1838 Dihedral : 4.288 26.271 1401 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.21 % Allowed : 17.42 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1285 helix: 1.03 (0.21), residues: 613 sheet: -0.72 (0.58), residues: 96 loop : -0.60 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 87 HIS 0.014 0.001 HIS B 10 PHE 0.019 0.001 PHE A 548 TYR 0.019 0.001 TYR L 337 ARG 0.004 0.000 ARG B 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6909 (mp0) REVERT: A 389 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7960 (tp30) REVERT: A 401 LYS cc_start: 0.6443 (mmmt) cc_final: 0.5563 (mmtp) REVERT: A 451 MET cc_start: 0.8593 (tpp) cc_final: 0.8354 (tpp) REVERT: A 535 LYS cc_start: 0.9279 (tppp) cc_final: 0.8966 (tppt) REVERT: A 566 MET cc_start: 0.6116 (mmm) cc_final: 0.4402 (tpp) REVERT: A 605 MET cc_start: 0.8165 (ppp) cc_final: 0.7726 (ppp) REVERT: A 699 LEU cc_start: 0.9425 (mt) cc_final: 0.9223 (mm) REVERT: B 32 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7915 (pp20) REVERT: B 42 GLN cc_start: 0.8271 (pm20) cc_final: 0.7740 (pm20) REVERT: B 45 TYR cc_start: 0.8376 (m-80) cc_final: 0.7898 (m-80) REVERT: C 111 ASP cc_start: 0.7725 (t0) cc_final: 0.7201 (m-30) REVERT: L 181 ASP cc_start: 0.6837 (m-30) cc_final: 0.6340 (t0) REVERT: L 204 ILE cc_start: 0.7264 (mt) cc_final: 0.6762 (mt) REVERT: L 247 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7396 (ttpt) REVERT: L 261 GLN cc_start: 0.7844 (pm20) cc_final: 0.7413 (pm20) REVERT: L 295 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6327 (mp0) REVERT: L 352 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6608 (pp) REVERT: R 48 HIS cc_start: 0.7085 (m-70) cc_final: 0.6485 (t70) REVERT: R 77 HIS cc_start: 0.4693 (m170) cc_final: 0.4438 (m170) outliers start: 26 outliers final: 20 residues processed: 192 average time/residue: 0.2277 time to fit residues: 63.0974 Evaluate side-chains 195 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain R residue 45 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.126926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.097411 restraints weight = 21684.974| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.38 r_work: 0.3671 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10695 Z= 0.212 Angle : 0.676 11.462 14455 Z= 0.342 Chirality : 0.042 0.187 1631 Planarity : 0.004 0.047 1838 Dihedral : 4.292 26.063 1401 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.70 % Allowed : 18.27 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1285 helix: 1.03 (0.21), residues: 612 sheet: -0.73 (0.58), residues: 96 loop : -0.63 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 27 HIS 0.005 0.001 HIS L 156 PHE 0.019 0.001 PHE A 548 TYR 0.017 0.001 TYR A 568 ARG 0.004 0.000 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6779.65 seconds wall clock time: 120 minutes 42.32 seconds (7242.32 seconds total)