Starting phenix.real_space_refine on Fri Sep 19 04:12:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn6_19388/09_2025/8rn6_19388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn6_19388/09_2025/8rn6_19388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rn6_19388/09_2025/8rn6_19388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn6_19388/09_2025/8rn6_19388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rn6_19388/09_2025/8rn6_19388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn6_19388/09_2025/8rn6_19388.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.113 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 S 90 5.16 5 C 7337 2.51 5 N 1955 2.21 5 O 2160 1.98 5 H 11505 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23047 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 11215 Classifications: {'peptide': 701} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 674} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 9935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 9935 Classifications: {'peptide': 634} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 600} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1897 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.27, per 1000 atoms: 0.19 Number of scatterers: 23047 At special positions: 0 Unit cell: (101.64, 118.44, 120.12, 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) S 90 16.00 O 2160 8.00 N 1955 7.00 C 7337 6.00 H 11505 1.00 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: 2.20 Conformation dependent library (CDL) restraints added in 616.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 50.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.571A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.942A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.595A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.838A pdb=" N ARG A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.750A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.155A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.609A pdb=" N GLU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 468 removed outlier: 3.654A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.511A pdb=" N ASP A 529 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 574 through 595 removed outlier: 4.366A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 3.673A pdb=" N ARG A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 716 removed outlier: 3.602A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.013A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.547A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.894A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.736A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.537A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.939A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.859A pdb=" N GLU B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.664A pdb=" N LEU B 588 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.631A pdb=" N ILE C 70 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.866A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.543A pdb=" N LEU A 110 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.840A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.178A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 323 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.178A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.000A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.313A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 189 removed outlier: 3.693A pdb=" N LYS B 202 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.860A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1608 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: 5.39 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11477 1.03 - 1.23: 36 1.23 - 1.42: 4850 1.42 - 1.62: 6773 1.62 - 1.81: 152 Bond restraints: 23288 Sorted by residual: bond pdb=" N VAL B 255 " pdb=" CA VAL B 255 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.68e+00 bond pdb=" C PHE B 251 " pdb=" O PHE B 251 " ideal model delta sigma weight residual 1.237 1.273 -0.036 1.31e-02 5.83e+03 7.55e+00 bond pdb=" N VAL B 254 " pdb=" H VAL B 254 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" N LEU B 253 " pdb=" H LEU B 253 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" N PHE B 251 " pdb=" H PHE B 251 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.96e+00 ... (remaining 23283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 39691 1.15 - 2.31: 2207 2.31 - 3.46: 169 3.46 - 4.62: 43 4.62 - 5.77: 6 Bond angle restraints: 42116 Sorted by residual: angle pdb=" CA VAL B 254 " pdb=" C VAL B 254 " pdb=" O VAL B 254 " ideal model delta sigma weight residual 120.95 116.76 4.19 1.04e+00 9.25e-01 1.63e+01 angle pdb=" N LYS B 189 " pdb=" CA LYS B 189 " pdb=" C LYS B 189 " ideal model delta sigma weight residual 108.74 113.94 -5.20 1.38e+00 5.25e-01 1.42e+01 angle pdb=" N ASN B 257 " pdb=" CA ASN B 257 " pdb=" C ASN B 257 " ideal model delta sigma weight residual 111.07 107.09 3.98 1.07e+00 8.73e-01 1.38e+01 angle pdb=" CA VAL B 252 " pdb=" C VAL B 252 " pdb=" O VAL B 252 " ideal model delta sigma weight residual 120.85 117.20 3.65 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CA VAL B 255 " pdb=" C VAL B 255 " pdb=" O VAL B 255 " ideal model delta sigma weight residual 120.95 117.81 3.14 1.04e+00 9.25e-01 9.12e+00 ... (remaining 42111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9559 17.82 - 35.64: 929 35.64 - 53.46: 339 53.46 - 71.27: 97 71.27 - 89.09: 13 Dihedral angle restraints: 10937 sinusoidal: 6000 harmonic: 4937 Sorted by residual: dihedral pdb=" CA LEU A 507 " pdb=" C LEU A 507 " pdb=" N ARG A 508 " pdb=" CA ARG A 508 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP B 93 " pdb=" CB ASP B 93 " pdb=" CG ASP B 93 " pdb=" OD1 ASP B 93 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP C 109 " pdb=" CB ASP C 109 " pdb=" CG ASP C 109 " pdb=" OD1 ASP C 109 " ideal model delta sinusoidal sigma weight residual -30.00 -87.96 57.96 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1366 0.042 - 0.084: 290 0.084 - 0.127: 71 0.127 - 0.169: 7 0.169 - 0.211: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CA LEU B 253 " pdb=" N LEU B 253 " pdb=" C LEU B 253 " pdb=" CB LEU B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 254 " pdb=" CA VAL B 254 " pdb=" CG1 VAL B 254 " pdb=" CG2 VAL B 254 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1732 not shown) Planarity restraints: 3422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 253 " 0.010 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" N VAL B 254 " -0.032 2.00e-02 2.50e+03 pdb=" CA VAL B 254 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL B 254 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 67 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 68 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 254 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C VAL B 254 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 254 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 255 " -0.009 2.00e-02 2.50e+03 ... (remaining 3419 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 492 2.08 - 2.71: 38559 2.71 - 3.34: 68000 3.34 - 3.97: 87473 3.97 - 4.60: 138549 Nonbonded interactions: 333073 Sorted by model distance: nonbonded pdb=" OE1 GLU A 378 " pdb=" H GLU A 378 " model vdw 1.456 2.450 nonbonded pdb=" O ASP B 305 " pdb=" H SER B 477 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASN A 563 " pdb="HE21 GLN A 566 " model vdw 1.597 2.450 nonbonded pdb=" O SER A 172 " pdb=" HG1 THR A 175 " model vdw 1.597 2.450 nonbonded pdb=" O GLU B 267 " pdb=" HZ1 LYS B 281 " model vdw 1.600 2.450 ... (remaining 333068 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: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11783 Z= 0.147 Angle : 0.571 5.771 15900 Z= 0.316 Chirality : 0.038 0.211 1735 Planarity : 0.004 0.053 2041 Dihedral : 17.606 89.093 4435 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.21 % Allowed : 26.01 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1439 helix: 1.52 (0.21), residues: 648 sheet: -0.93 (0.39), residues: 161 loop : -0.90 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 135 TYR 0.014 0.001 TYR B 466 PHE 0.009 0.001 PHE B 251 TRP 0.011 0.001 TRP B 437 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00307 (11783) covalent geometry : angle 0.57072 (15900) hydrogen bonds : bond 0.13980 ( 569) hydrogen bonds : angle 5.63725 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLN cc_start: 0.8277 (mt0) cc_final: 0.8045 (mt0) outliers start: 28 outliers final: 24 residues processed: 188 average time/residue: 1.3404 time to fit residues: 273.6163 Evaluate side-chains 182 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 276 ASN ** B 517 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 = 0.4032 r_free = 0.4032 target = 0.172858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124380 restraints weight = 37196.699| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.93 r_work: 0.3306 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11783 Z= 0.184 Angle : 0.567 5.205 15900 Z= 0.298 Chirality : 0.040 0.166 1735 Planarity : 0.004 0.046 2041 Dihedral : 6.420 58.624 1602 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.40 % Allowed : 23.64 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.22), residues: 1439 helix: 1.29 (0.20), residues: 666 sheet: -0.85 (0.40), residues: 171 loop : -0.89 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 93 TYR 0.016 0.001 TYR B 554 PHE 0.010 0.001 PHE C 113 TRP 0.016 0.002 TRP B 437 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00435 (11783) covalent geometry : angle 0.56674 (15900) hydrogen bonds : bond 0.04948 ( 569) hydrogen bonds : angle 4.82668 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8348 (p0) cc_final: 0.8147 (p0) REVERT: A 478 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8765 (p) REVERT: B 268 GLN cc_start: 0.8804 (mt0) cc_final: 0.8594 (mt0) outliers start: 43 outliers final: 23 residues processed: 197 average time/residue: 1.3379 time to fit residues: 286.5652 Evaluate side-chains 186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.173455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129906 restraints weight = 36990.574| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.82 r_work: 0.3387 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11783 Z= 0.136 Angle : 0.536 5.660 15900 Z= 0.279 Chirality : 0.038 0.160 1735 Planarity : 0.004 0.049 2041 Dihedral : 5.719 58.716 1586 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.32 % Allowed : 23.48 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1439 helix: 1.37 (0.20), residues: 664 sheet: -0.77 (0.40), residues: 169 loop : -0.94 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 622 TYR 0.015 0.001 TYR B 554 PHE 0.009 0.001 PHE C 113 TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00316 (11783) covalent geometry : angle 0.53610 (15900) hydrogen bonds : bond 0.04264 ( 569) hydrogen bonds : angle 4.62190 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8554 (tpt) cc_final: 0.8237 (tpt) REVERT: A 478 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 501 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8633 (p) REVERT: B 268 GLN cc_start: 0.8794 (mt0) cc_final: 0.8565 (mt0) REVERT: B 511 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.4832 (t80) outliers start: 42 outliers final: 21 residues processed: 198 average time/residue: 1.2843 time to fit residues: 277.5900 Evaluate side-chains 183 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 566 GLN B 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.173724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125633 restraints weight = 37041.526| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.92 r_work: 0.3323 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11783 Z= 0.124 Angle : 0.528 5.325 15900 Z= 0.273 Chirality : 0.038 0.159 1735 Planarity : 0.004 0.054 2041 Dihedral : 5.555 59.254 1583 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 2.92 % Allowed : 23.64 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1439 helix: 1.44 (0.20), residues: 665 sheet: -0.60 (0.41), residues: 164 loop : -0.97 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 622 TYR 0.015 0.001 TYR B 554 PHE 0.008 0.001 PHE B 511 TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00294 (11783) covalent geometry : angle 0.52766 (15900) hydrogen bonds : bond 0.03916 ( 569) hydrogen bonds : angle 4.46512 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.1891 (mpp) REVERT: A 501 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8621 (p) REVERT: A 506 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.5806 (t-170) REVERT: A 528 VAL cc_start: 0.9041 (m) cc_final: 0.8720 (t) REVERT: B 268 GLN cc_start: 0.8813 (mt0) cc_final: 0.8578 (mt0) REVERT: B 353 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7969 (mttm) REVERT: B 511 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.4799 (t80) REVERT: C 115 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7173 (ttp80) outliers start: 37 outliers final: 24 residues processed: 192 average time/residue: 1.2924 time to fit residues: 270.5305 Evaluate side-chains 186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125046 restraints weight = 36981.855| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.91 r_work: 0.3319 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11783 Z= 0.141 Angle : 0.534 5.649 15900 Z= 0.276 Chirality : 0.039 0.160 1735 Planarity : 0.004 0.067 2041 Dihedral : 5.545 58.098 1583 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 3.64 % Allowed : 22.77 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1439 helix: 1.42 (0.20), residues: 666 sheet: -0.58 (0.41), residues: 164 loop : -0.99 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 622 TYR 0.015 0.001 TYR B 554 PHE 0.009 0.001 PHE C 113 TRP 0.013 0.001 TRP B 437 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00339 (11783) covalent geometry : angle 0.53403 (15900) hydrogen bonds : bond 0.03985 ( 569) hydrogen bonds : angle 4.41953 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.4592 (OUTLIER) cc_final: 0.2046 (mpp) REVERT: A 501 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8621 (p) REVERT: A 506 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.5804 (t-170) REVERT: A 528 VAL cc_start: 0.9028 (m) cc_final: 0.8743 (t) REVERT: B 353 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8030 (mttm) REVERT: B 511 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.4811 (t80) REVERT: C 115 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7225 (ttp80) outliers start: 46 outliers final: 28 residues processed: 194 average time/residue: 1.2875 time to fit residues: 272.6797 Evaluate side-chains 189 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.0030 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.173628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126514 restraints weight = 36693.687| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.85 r_work: 0.3336 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11783 Z= 0.157 Angle : 0.542 5.489 15900 Z= 0.282 Chirality : 0.039 0.162 1735 Planarity : 0.004 0.079 2041 Dihedral : 5.481 59.810 1582 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.79 % Allowed : 22.06 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1439 helix: 1.38 (0.20), residues: 667 sheet: -0.55 (0.41), residues: 164 loop : -0.99 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 622 TYR 0.016 0.001 TYR B 554 PHE 0.009 0.001 PHE B 550 TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00379 (11783) covalent geometry : angle 0.54243 (15900) hydrogen bonds : bond 0.04051 ( 569) hydrogen bonds : angle 4.39908 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4594 (OUTLIER) cc_final: 0.2073 (mpp) REVERT: A 501 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 506 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.5864 (t-170) REVERT: A 528 VAL cc_start: 0.9063 (m) cc_final: 0.8787 (t) REVERT: B 353 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8074 (mttm) REVERT: B 511 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: C 115 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6983 (ttp80) REVERT: C 128 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7063 (m-30) outliers start: 48 outliers final: 30 residues processed: 195 average time/residue: 1.3323 time to fit residues: 282.8403 Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128229 restraints weight = 36636.078| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.86 r_work: 0.3358 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11783 Z= 0.109 Angle : 0.520 5.682 15900 Z= 0.269 Chirality : 0.038 0.160 1735 Planarity : 0.004 0.083 2041 Dihedral : 5.386 59.136 1582 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.08 % Allowed : 22.92 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1439 helix: 1.48 (0.20), residues: 670 sheet: -0.68 (0.42), residues: 154 loop : -0.93 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 622 TYR 0.014 0.001 TYR C 74 PHE 0.008 0.001 PHE C 113 TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00254 (11783) covalent geometry : angle 0.51978 (15900) hydrogen bonds : bond 0.03641 ( 569) hydrogen bonds : angle 4.31207 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4598 (OUTLIER) cc_final: 0.2088 (mpp) REVERT: A 294 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8093 (ttp) REVERT: A 501 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 506 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5828 (t-170) REVERT: A 528 VAL cc_start: 0.8975 (m) cc_final: 0.8728 (t) REVERT: B 353 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8009 (mttm) REVERT: B 511 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5762 (m-80) outliers start: 39 outliers final: 21 residues processed: 193 average time/residue: 1.3372 time to fit residues: 281.2181 Evaluate side-chains 184 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123875 restraints weight = 36633.982| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.87 r_work: 0.3006 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11783 Z= 0.127 Angle : 0.524 5.973 15900 Z= 0.271 Chirality : 0.038 0.160 1735 Planarity : 0.004 0.093 2041 Dihedral : 5.135 56.828 1578 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.85 % Allowed : 23.32 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1439 helix: 1.48 (0.20), residues: 670 sheet: -0.66 (0.42), residues: 154 loop : -0.93 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 622 TYR 0.014 0.001 TYR B 554 PHE 0.008 0.001 PHE B 511 TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00304 (11783) covalent geometry : angle 0.52447 (15900) hydrogen bonds : bond 0.03725 ( 569) hydrogen bonds : angle 4.28053 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4611 (OUTLIER) cc_final: 0.2114 (mpp) REVERT: A 294 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: A 501 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 506 HIS cc_start: 0.6765 (OUTLIER) cc_final: 0.5800 (t-170) REVERT: A 528 VAL cc_start: 0.8931 (m) cc_final: 0.8715 (t) REVERT: B 353 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7975 (mtmm) REVERT: B 511 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5729 (m-80) outliers start: 36 outliers final: 24 residues processed: 188 average time/residue: 1.3395 time to fit residues: 274.2405 Evaluate side-chains 184 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN B 306 ASN ** B 604 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.173814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126598 restraints weight = 36568.234| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.86 r_work: 0.3336 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11783 Z= 0.151 Angle : 0.543 6.305 15900 Z= 0.281 Chirality : 0.039 0.163 1735 Planarity : 0.004 0.088 2041 Dihedral : 4.912 56.571 1576 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.16 % Allowed : 23.08 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1439 helix: 1.42 (0.20), residues: 670 sheet: -0.71 (0.42), residues: 154 loop : -0.95 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 622 TYR 0.015 0.001 TYR B 554 PHE 0.008 0.001 PHE B 550 TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00364 (11783) covalent geometry : angle 0.54308 (15900) hydrogen bonds : bond 0.03884 ( 569) hydrogen bonds : angle 4.30137 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.2185 (mpp) REVERT: A 294 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8121 (ttp) REVERT: A 501 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 506 HIS cc_start: 0.6780 (OUTLIER) cc_final: 0.5834 (t-170) REVERT: A 528 VAL cc_start: 0.9017 (m) cc_final: 0.8780 (t) REVERT: B 353 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8123 (mtmm) REVERT: B 511 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5761 (m-80) outliers start: 40 outliers final: 27 residues processed: 191 average time/residue: 1.2876 time to fit residues: 267.9210 Evaluate side-chains 185 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 144 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128428 restraints weight = 37045.780| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.84 r_work: 0.2994 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11783 Z= 0.141 Angle : 0.536 6.604 15900 Z= 0.277 Chirality : 0.039 0.162 1735 Planarity : 0.004 0.087 2041 Dihedral : 4.895 56.087 1576 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 2.69 % Allowed : 23.64 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1439 helix: 1.41 (0.20), residues: 671 sheet: -0.69 (0.42), residues: 154 loop : -0.94 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 135 TYR 0.016 0.001 TYR C 74 PHE 0.008 0.001 PHE B 511 TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00338 (11783) covalent geometry : angle 0.53618 (15900) hydrogen bonds : bond 0.03815 ( 569) hydrogen bonds : angle 4.27709 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4736 (OUTLIER) cc_final: 0.2260 (mpp) REVERT: A 143 MET cc_start: 0.6423 (mtt) cc_final: 0.6088 (mtt) REVERT: A 294 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8146 (ttp) REVERT: A 501 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8548 (p) REVERT: A 506 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.5854 (t-170) REVERT: A 528 VAL cc_start: 0.8958 (m) cc_final: 0.8747 (t) REVERT: B 135 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7331 (mtm110) REVERT: B 353 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8054 (mtmm) REVERT: B 511 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5702 (m-80) outliers start: 34 outliers final: 23 residues processed: 185 average time/residue: 1.1123 time to fit residues: 225.4538 Evaluate side-chains 183 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 137 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129272 restraints weight = 36850.878| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.84 r_work: 0.3011 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11783 Z= 0.115 Angle : 0.529 6.624 15900 Z= 0.273 Chirality : 0.038 0.160 1735 Planarity : 0.004 0.086 2041 Dihedral : 4.819 55.778 1576 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 2.69 % Allowed : 23.72 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.22), residues: 1439 helix: 1.53 (0.20), residues: 670 sheet: -0.61 (0.42), residues: 154 loop : -0.89 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 622 TYR 0.017 0.001 TYR C 74 PHE 0.008 0.001 PHE C 113 TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00276 (11783) covalent geometry : angle 0.52928 (15900) hydrogen bonds : bond 0.03564 ( 569) hydrogen bonds : angle 4.20803 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9210.45 seconds wall clock time: 156 minutes 39.15 seconds (9399.15 seconds total)