Starting phenix.real_space_refine on Sun Oct 12 21:47:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k90_36970/10_2025/8k90_36970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k90_36970/10_2025/8k90_36970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k90_36970/10_2025/8k90_36970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k90_36970/10_2025/8k90_36970.map" model { file = "/net/cci-nas-00/data/ceres_data/8k90_36970/10_2025/8k90_36970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k90_36970/10_2025/8k90_36970.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 P 3 5.49 5 S 38 5.16 5 C 17625 2.51 5 N 5000 2.21 5 O 5229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27895 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.61, per 1000 atoms: 0.24 Number of scatterers: 27895 At special positions: 0 Unit cell: (129.56, 162.36, 175.48, 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 38 16.00 P 3 15.00 O 5229 8.00 N 5000 7.00 C 17625 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: 2.20 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 58 sheets defined 53.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.558A pdb=" N ARG A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.554A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.539A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.513A pdb=" N ASN A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.877A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.572A pdb=" N LEU A 547 " --> pdb=" O HIS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 649 through 653 removed outlier: 3.926A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 121 through 153 removed outlier: 3.758A pdb=" N ALA B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.626A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.778A pdb=" N GLY B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.509A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 4.021A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 585 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 653 removed outlier: 4.140A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.547A pdb=" N LEU B 661 " --> pdb=" O ARG B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 70 Processing helix chain 'C' and resid 97 through 119 removed outlier: 4.111A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 removed outlier: 3.531A pdb=" N LEU C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.251A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.751A pdb=" N ARG C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 471 removed outlier: 4.171A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 532 through 534 No H-bonds generated for 'chain 'C' and resid 532 through 534' Processing helix chain 'C' and resid 543 through 557 Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 636 removed outlier: 3.516A pdb=" N LYS C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 653 removed outlier: 4.291A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 58 through 70 Processing helix chain 'D' and resid 97 through 119 removed outlier: 4.010A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 153 removed outlier: 3.558A pdb=" N LEU D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.208A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 313 through 320 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.625A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 4.033A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 543 through 557 Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 653 removed outlier: 4.190A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.648A pdb=" N SER E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 4.427A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 153 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.647A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.526A pdb=" N PHE E 367 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.537A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.536A pdb=" N ARG E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 543 through 557 removed outlier: 3.902A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 637 removed outlier: 3.625A pdb=" N LYS E 625 " --> pdb=" O ALA E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.079A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 removed outlier: 3.502A pdb=" N LEU E 661 " --> pdb=" O ARG E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.374A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLU A 269 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N HIS A 48 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ALA A 384 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR A 50 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.094A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 504 Processing sheet with id=AB2, first strand: chain 'A' and resid 583 through 584 removed outlier: 4.577A pdb=" N ALA A 583 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 604 through 606 removed outlier: 6.490A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN A 642 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR A 672 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.342A pdb=" N VAL B 267 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP B 313 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR B 50 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 160 removed outlier: 4.209A pdb=" N ARG B 163 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AB8, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB9, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AC1, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AC2, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.528A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AC4, first strand: chain 'B' and resid 498 through 504 Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 584 removed outlier: 4.338A pdb=" N ALA B 583 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 609 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 604 through 606 removed outlier: 6.976A pdb=" N GLN B 642 " --> pdb=" O HIS B 670 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR B 672 " --> pdb=" O GLN B 642 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.771A pdb=" N ILE C 671 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN C 642 " --> pdb=" O HIS C 670 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR C 672 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.396A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLU C 269 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA C 49 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N GLY C 362 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 51 " --> pdb=" O GLY C 362 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 77 through 82 Processing sheet with id=AD1, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AD2, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AD3, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AD4, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AD5, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AD6, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.267A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AD8, first strand: chain 'C' and resid 498 through 504 removed outlier: 6.919A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.413A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 609 " --> pdb=" O LEU C 617 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 49 through 52 removed outlier: 7.136A pdb=" N ALA D 49 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N GLY D 362 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU D 51 " --> pdb=" O GLY D 362 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AE3, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AE4, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AE5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AE6, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AE7, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AE8, first strand: chain 'D' and resid 410 through 411 removed outlier: 6.616A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AF1, first strand: chain 'D' and resid 529 through 530 removed outlier: 10.405A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN D 642 " --> pdb=" O HIS D 670 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N TYR D 672 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.617A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 609 " --> pdb=" O LEU D 617 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 266 through 269 removed outlier: 3.625A pdb=" N ASP E 313 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AF5, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AF6, first strand: chain 'E' and resid 297 through 298 removed outlier: 3.676A pdb=" N ARG E 280 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF8, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AF9, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AG1, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AG2, first strand: chain 'E' and resid 498 through 504 Processing sheet with id=AG3, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.726A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 609 " --> pdb=" O LEU E 617 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.121A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 1550 hydrogen bonds defined for protein. 4506 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: 6.60 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 9754 1.36 - 1.50: 7119 1.50 - 1.65: 11511 1.65 - 1.80: 41 1.80 - 1.95: 22 Bond restraints: 28447 Sorted by residual: bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.945 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" O4P TS6 D 801 " pdb=" P TS6 D 801 " ideal model delta sigma weight residual 1.516 1.610 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " ideal model delta sigma weight residual 1.516 1.610 -0.094 2.00e-02 2.50e+03 2.20e+01 ... (remaining 28442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 38410 3.45 - 6.91: 196 6.91 - 10.36: 3 10.36 - 13.81: 10 13.81 - 17.26: 4 Bond angle restraints: 38623 Sorted by residual: angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.41 -17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" N LEU B 57 " pdb=" CA LEU B 57 " pdb=" C LEU B 57 " ideal model delta sigma weight residual 113.16 106.69 6.47 1.24e+00 6.50e-01 2.72e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" O3P TS6 C 801 " ideal model delta sigma weight residual 116.25 101.10 15.15 3.00e+00 1.11e-01 2.55e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" O4P TS6 D 801 " ideal model delta sigma weight residual 116.34 101.46 14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" N ASN D 332 " pdb=" CA ASN D 332 " pdb=" C ASN D 332 " ideal model delta sigma weight residual 113.16 107.09 6.07 1.24e+00 6.50e-01 2.40e+01 ... (remaining 38618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15738 18.00 - 35.99: 1106 35.99 - 53.99: 189 53.99 - 71.98: 135 71.98 - 89.98: 102 Dihedral angle restraints: 17270 sinusoidal: 6995 harmonic: 10275 Sorted by residual: dihedral pdb=" CA ILE B 558 " pdb=" C ILE B 558 " pdb=" N GLU B 559 " pdb=" CA GLU B 559 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU C 127 " pdb=" C GLU C 127 " pdb=" N LYS C 128 " pdb=" CA LYS C 128 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA MET B 356 " pdb=" C MET B 356 " pdb=" N GLN B 357 " pdb=" CA GLN B 357 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 17267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3580 0.052 - 0.104: 586 0.104 - 0.156: 112 0.156 - 0.207: 17 0.207 - 0.259: 10 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA LEU B 360 " pdb=" N LEU B 360 " pdb=" C LEU B 360 " pdb=" CB LEU B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL B 267 " pdb=" N VAL B 267 " pdb=" C VAL B 267 " pdb=" CB VAL B 267 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU D 360 " pdb=" N LEU D 360 " pdb=" C LEU D 360 " pdb=" CB LEU D 360 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4302 not shown) Planarity restraints: 5155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 373 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO C 374 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO C 374 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 374 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 54 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 55 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 127 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C GLU C 127 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU C 127 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS C 128 " 0.014 2.00e-02 2.50e+03 ... (remaining 5152 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 327 2.64 - 3.21: 26495 3.21 - 3.77: 46936 3.77 - 4.34: 62557 4.34 - 4.90: 101395 Nonbonded interactions: 237710 Sorted by model distance: nonbonded pdb=" OG SER D 471 " pdb=" OH TYR D 510 " model vdw 2.078 3.040 nonbonded pdb=" OG1 THR B 256 " pdb=" O HIS B 303 " model vdw 2.081 3.040 nonbonded pdb=" O ALA D 447 " pdb=" OG SER D 459 " model vdw 2.113 3.040 nonbonded pdb=" O ALA A 447 " pdb=" OG SER A 459 " model vdw 2.118 3.040 nonbonded pdb=" NH2 ARG D 488 " pdb=" OE1 GLU E 648 " model vdw 2.161 3.120 ... (remaining 237705 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 719) selection = (chain 'C' and resid 1 through 719) selection = (chain 'D' and resid 1 through 719) selection = chain 'E' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.150 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 0.330 28447 Z= 0.292 Angle : 0.737 17.265 38623 Z= 0.424 Chirality : 0.043 0.259 4305 Planarity : 0.005 0.115 5155 Dihedral : 15.931 89.977 10670 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.14 % Allowed : 0.25 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.14), residues: 3585 helix: 1.75 (0.12), residues: 1824 sheet: 0.09 (0.26), residues: 412 loop : -0.31 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 134 TYR 0.023 0.002 TYR C 50 PHE 0.019 0.001 PHE B 629 TRP 0.024 0.002 TRP C 205 HIS 0.006 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00542 (28447) covalent geometry : angle 0.73661 (38623) hydrogen bonds : bond 0.13973 ( 1550) hydrogen bonds : angle 5.97902 ( 4506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 486 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.5332 (tt0) cc_final: 0.4895 (mm-30) REVERT: A 200 ARG cc_start: 0.7593 (tpp-160) cc_final: 0.7341 (ptt90) REVERT: A 205 TRP cc_start: 0.7299 (m100) cc_final: 0.6900 (m100) REVERT: A 213 ARG cc_start: 0.4065 (mmm-85) cc_final: 0.3774 (tpt170) REVERT: A 276 ARG cc_start: 0.6735 (mtp180) cc_final: 0.6502 (mmt90) REVERT: A 303 HIS cc_start: 0.7220 (m-70) cc_final: 0.6579 (m-70) REVERT: A 356 MET cc_start: 0.6603 (mpp) cc_final: 0.6213 (mtp) REVERT: A 534 GLU cc_start: 0.5875 (mp0) cc_final: 0.5230 (mt-10) REVERT: A 676 THR cc_start: 0.8388 (p) cc_final: 0.8186 (p) REVERT: B 37 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6890 (pt0) REVERT: B 87 LYS cc_start: 0.8265 (ttpp) cc_final: 0.8000 (tptt) REVERT: B 201 LEU cc_start: 0.8497 (tp) cc_final: 0.7958 (mp) REVERT: B 203 ARG cc_start: 0.7246 (tpt170) cc_final: 0.6658 (tpt170) REVERT: B 215 GLU cc_start: 0.9338 (pt0) cc_final: 0.9052 (pt0) REVERT: B 218 PHE cc_start: 0.8107 (m-10) cc_final: 0.7787 (m-10) REVERT: B 232 ARG cc_start: 0.8289 (ttp-170) cc_final: 0.8049 (tmm-80) REVERT: B 282 ASP cc_start: 0.8057 (m-30) cc_final: 0.7234 (m-30) REVERT: B 331 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7694 (mmm160) REVERT: B 334 GLN cc_start: 0.8177 (mt0) cc_final: 0.7924 (mp-120) REVERT: B 348 GLU cc_start: 0.8017 (tt0) cc_final: 0.7152 (tp30) REVERT: B 351 PRO cc_start: 0.6712 (Cg_exo) cc_final: 0.6500 (Cg_endo) REVERT: B 382 ILE cc_start: 0.7729 (mm) cc_final: 0.7439 (mm) REVERT: B 710 GLU cc_start: 0.4909 (mt-10) cc_final: 0.4667 (tp30) REVERT: C 211 ASN cc_start: 0.8298 (m-40) cc_final: 0.7660 (m110) REVERT: C 215 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8786 (mm-30) REVERT: C 257 SER cc_start: 0.6834 (m) cc_final: 0.6586 (p) REVERT: C 269 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7184 (mm-30) REVERT: C 271 TYR cc_start: 0.6882 (t80) cc_final: 0.6615 (t80) REVERT: C 334 GLN cc_start: 0.8191 (mt0) cc_final: 0.7900 (mt0) REVERT: C 342 GLN cc_start: 0.7328 (pt0) cc_final: 0.6975 (mp10) REVERT: C 494 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8369 (mtt-85) REVERT: C 579 GLU cc_start: 0.5246 (mp0) cc_final: 0.4872 (pm20) REVERT: C 582 SER cc_start: 0.7246 (p) cc_final: 0.6816 (p) REVERT: C 662 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7744 (mt-10) REVERT: D 387 SER cc_start: 0.8416 (t) cc_final: 0.8158 (p) REVERT: D 454 LEU cc_start: 0.8332 (tt) cc_final: 0.7844 (mm) REVERT: D 458 GLU cc_start: 0.8684 (mp0) cc_final: 0.8389 (mp0) REVERT: D 567 ILE cc_start: 0.6232 (mt) cc_final: 0.5981 (mt) REVERT: D 606 VAL cc_start: 0.6825 (t) cc_final: 0.6563 (m) REVERT: E 6 GLU cc_start: 0.7279 (pp20) cc_final: 0.6794 (mm-30) REVERT: E 52 VAL cc_start: 0.8470 (t) cc_final: 0.8240 (t) REVERT: E 157 LEU cc_start: 0.6604 (tp) cc_final: 0.6363 (tp) REVERT: E 179 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7331 (mmm160) REVERT: E 283 TYR cc_start: 0.5394 (m-80) cc_final: 0.5097 (m-80) REVERT: E 309 TYR cc_start: 0.7501 (m-80) cc_final: 0.7297 (m-80) REVERT: E 348 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8133 (tt0) REVERT: E 368 GLU cc_start: 0.5268 (mm-30) cc_final: 0.4728 (mt-10) REVERT: E 383 ARG cc_start: 0.6987 (ttt90) cc_final: 0.6570 (ttm-80) REVERT: E 475 GLU cc_start: 0.4867 (mm-30) cc_final: 0.4640 (mp0) REVERT: E 662 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8632 (mm-30) outliers start: 4 outliers final: 1 residues processed: 488 average time/residue: 0.2195 time to fit residues: 160.0301 Evaluate side-chains 267 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.189567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134684 restraints weight = 48756.317| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 4.01 r_work: 0.3592 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28447 Z= 0.162 Angle : 0.599 8.410 38623 Z= 0.304 Chirality : 0.040 0.202 4305 Planarity : 0.005 0.065 5155 Dihedral : 4.181 44.278 4002 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.30 % Allowed : 7.57 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.14), residues: 3585 helix: 1.68 (0.12), residues: 1852 sheet: -0.01 (0.26), residues: 422 loop : -0.35 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 126 TYR 0.022 0.002 TYR C 50 PHE 0.021 0.002 PHE C 119 TRP 0.028 0.002 TRP E 250 HIS 0.006 0.001 HIS E 469 Details of bonding type rmsd covalent geometry : bond 0.00367 (28447) covalent geometry : angle 0.59855 (38623) hydrogen bonds : bond 0.04340 ( 1550) hydrogen bonds : angle 4.81174 ( 4506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.5116 (m-80) cc_final: 0.3955 (m-10) REVERT: A 64 LEU cc_start: 0.7529 (mm) cc_final: 0.6812 (tt) REVERT: A 118 LEU cc_start: 0.3289 (OUTLIER) cc_final: 0.2716 (mt) REVERT: A 128 LYS cc_start: 0.2549 (mmtm) cc_final: 0.2015 (mmtt) REVERT: A 193 GLU cc_start: 0.4944 (tt0) cc_final: 0.4278 (mm-30) REVERT: A 200 ARG cc_start: 0.7504 (tpp-160) cc_final: 0.7260 (ptt90) REVERT: A 225 ARG cc_start: 0.7395 (mmm160) cc_final: 0.7028 (mtm110) REVERT: A 276 ARG cc_start: 0.6573 (mtp180) cc_final: 0.6289 (mmt90) REVERT: A 303 HIS cc_start: 0.7478 (m-70) cc_final: 0.6862 (m170) REVERT: A 426 MET cc_start: 0.7215 (mtm) cc_final: 0.6918 (mtm) REVERT: A 534 GLU cc_start: 0.5955 (mp0) cc_final: 0.5060 (mt-10) REVERT: B 37 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7384 (pt0) REVERT: B 87 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8086 (tptt) REVERT: B 201 LEU cc_start: 0.8431 (tp) cc_final: 0.8109 (mt) REVERT: B 217 LEU cc_start: 0.8544 (mt) cc_final: 0.8079 (mt) REVERT: B 232 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7904 (ptm160) REVERT: B 282 ASP cc_start: 0.8388 (m-30) cc_final: 0.7882 (t0) REVERT: B 296 LEU cc_start: 0.8437 (mt) cc_final: 0.7732 (tp) REVERT: B 334 GLN cc_start: 0.8239 (mt0) cc_final: 0.7989 (mp-120) REVERT: B 348 GLU cc_start: 0.8023 (tt0) cc_final: 0.7251 (tp30) REVERT: B 351 PRO cc_start: 0.6630 (Cg_exo) cc_final: 0.6422 (Cg_endo) REVERT: B 382 ILE cc_start: 0.7910 (mm) cc_final: 0.7668 (mm) REVERT: C 211 ASN cc_start: 0.8305 (m-40) cc_final: 0.7703 (m110) REVERT: C 215 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 269 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 319 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7811 (ttp80) REVERT: C 327 LYS cc_start: 0.7589 (ttpt) cc_final: 0.7326 (ttpt) REVERT: C 334 GLN cc_start: 0.8321 (mt0) cc_final: 0.8065 (mt0) REVERT: C 342 GLN cc_start: 0.7418 (pt0) cc_final: 0.7152 (mp10) REVERT: C 395 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7938 (tp30) REVERT: C 405 LEU cc_start: 0.8470 (tp) cc_final: 0.8164 (mm) REVERT: C 494 ARG cc_start: 0.8864 (mtt-85) cc_final: 0.8627 (mtt-85) REVERT: C 579 GLU cc_start: 0.5507 (mp0) cc_final: 0.5144 (pm20) REVERT: D 219 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6777 (mp10) REVERT: D 454 LEU cc_start: 0.8373 (tt) cc_final: 0.7880 (mm) REVERT: E 6 GLU cc_start: 0.7063 (pp20) cc_final: 0.6560 (mm-30) REVERT: E 52 VAL cc_start: 0.8726 (t) cc_final: 0.8439 (t) REVERT: E 103 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: E 205 TRP cc_start: 0.8023 (m100) cc_final: 0.7272 (m-10) REVERT: E 231 LEU cc_start: 0.8163 (tp) cc_final: 0.7962 (mt) REVERT: E 241 THR cc_start: 0.7310 (m) cc_final: 0.7101 (m) REVERT: E 323 TRP cc_start: 0.7882 (t-100) cc_final: 0.7609 (t-100) REVERT: E 348 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8272 (tt0) REVERT: E 368 GLU cc_start: 0.5286 (mm-30) cc_final: 0.4919 (mt-10) REVERT: E 383 ARG cc_start: 0.7161 (ttt90) cc_final: 0.6511 (ttm-80) REVERT: E 385 GLU cc_start: 0.6505 (mt-10) cc_final: 0.5629 (tt0) REVERT: E 475 GLU cc_start: 0.4979 (mm-30) cc_final: 0.4672 (mp0) outliers start: 37 outliers final: 29 residues processed: 331 average time/residue: 0.2086 time to fit residues: 107.1379 Evaluate side-chains 272 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 689 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 52 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 150 optimal weight: 0.0020 chunk 192 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 overall best weight: 0.9350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.193217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.156150 restraints weight = 49204.619| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 3.65 r_work: 0.3634 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28447 Z= 0.127 Angle : 0.548 9.035 38623 Z= 0.278 Chirality : 0.039 0.166 4305 Planarity : 0.004 0.058 5155 Dihedral : 4.056 44.395 4002 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.34 % Allowed : 9.72 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.14), residues: 3585 helix: 1.73 (0.12), residues: 1855 sheet: 0.08 (0.26), residues: 422 loop : -0.29 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 200 TYR 0.024 0.002 TYR B 271 PHE 0.016 0.001 PHE D 135 TRP 0.022 0.002 TRP A 403 HIS 0.006 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00279 (28447) covalent geometry : angle 0.54843 (38623) hydrogen bonds : bond 0.03932 ( 1550) hydrogen bonds : angle 4.53994 ( 4506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7526 (mm) cc_final: 0.6663 (tt) REVERT: A 193 GLU cc_start: 0.4705 (tt0) cc_final: 0.4038 (mm-30) REVERT: A 205 TRP cc_start: 0.6689 (t-100) cc_final: 0.6246 (t-100) REVERT: A 225 ARG cc_start: 0.7097 (mmm160) cc_final: 0.6896 (mtm110) REVERT: A 276 ARG cc_start: 0.6572 (mtp180) cc_final: 0.6352 (mmt90) REVERT: A 303 HIS cc_start: 0.7171 (m-70) cc_final: 0.6785 (m170) REVERT: A 318 LYS cc_start: 0.6595 (pttm) cc_final: 0.5806 (tptp) REVERT: A 534 GLU cc_start: 0.5611 (mp0) cc_final: 0.4843 (mt-10) REVERT: A 574 ASN cc_start: 0.6625 (p0) cc_final: 0.6030 (t0) REVERT: A 623 ASN cc_start: 0.6696 (p0) cc_final: 0.6213 (p0) REVERT: A 678 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: B 57 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 201 LEU cc_start: 0.8416 (tp) cc_final: 0.8062 (mt) REVERT: B 217 LEU cc_start: 0.8473 (mt) cc_final: 0.8085 (mt) REVERT: B 348 GLU cc_start: 0.7899 (tt0) cc_final: 0.7405 (tp30) REVERT: C 132 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7726 (pp20) REVERT: C 211 ASN cc_start: 0.8089 (m-40) cc_final: 0.7493 (m110) REVERT: C 215 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 269 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7747 (mm-30) REVERT: C 271 TYR cc_start: 0.7284 (t80) cc_final: 0.6888 (t80) REVERT: C 405 LEU cc_start: 0.8476 (tp) cc_final: 0.8234 (mm) REVERT: D 219 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6985 (mm-40) REVERT: E 6 GLU cc_start: 0.6933 (pp20) cc_final: 0.6449 (mm-30) REVERT: E 205 TRP cc_start: 0.7860 (m100) cc_final: 0.7138 (m-10) REVERT: E 231 LEU cc_start: 0.8196 (tp) cc_final: 0.7992 (mt) REVERT: E 383 ARG cc_start: 0.7295 (ttt90) cc_final: 0.6855 (ttm-80) REVERT: E 385 GLU cc_start: 0.6423 (mt-10) cc_final: 0.5859 (tt0) REVERT: E 472 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6292 (m-10) REVERT: E 549 LEU cc_start: 0.8454 (mm) cc_final: 0.8128 (mm) outliers start: 38 outliers final: 23 residues processed: 296 average time/residue: 0.2003 time to fit residues: 92.3987 Evaluate side-chains 238 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 324 optimal weight: 9.9990 chunk 351 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 51 optimal weight: 0.0570 chunk 296 optimal weight: 30.0000 chunk 181 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 253 ASN B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 696 GLN D 211 ASN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.141851 restraints weight = 49098.113| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.75 r_work: 0.3597 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 28447 Z= 0.298 Angle : 0.681 11.651 38623 Z= 0.343 Chirality : 0.043 0.162 4305 Planarity : 0.005 0.062 5155 Dihedral : 4.396 44.537 4002 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.29 % Allowed : 11.34 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.75 (0.14), residues: 3585 helix: 1.44 (0.12), residues: 1862 sheet: -0.34 (0.25), residues: 430 loop : -0.51 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 488 TYR 0.030 0.003 TYR C 50 PHE 0.029 0.002 PHE A 630 TRP 0.030 0.003 TRP A 403 HIS 0.013 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00697 (28447) covalent geometry : angle 0.68101 (38623) hydrogen bonds : bond 0.04267 ( 1550) hydrogen bonds : angle 4.83242 ( 4506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.2536 (mt) cc_final: 0.1934 (mt) REVERT: A 193 GLU cc_start: 0.4614 (tt0) cc_final: 0.3841 (mm-30) REVERT: A 205 TRP cc_start: 0.6713 (t-100) cc_final: 0.6240 (t-100) REVERT: A 217 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7835 (mm) REVERT: A 416 LEU cc_start: 0.7309 (tt) cc_final: 0.6997 (tt) REVERT: A 534 GLU cc_start: 0.5645 (mp0) cc_final: 0.5076 (mt-10) REVERT: A 558 ILE cc_start: 0.4554 (OUTLIER) cc_final: 0.3913 (tp) REVERT: A 623 ASN cc_start: 0.6946 (p0) cc_final: 0.6532 (p0) REVERT: A 642 GLN cc_start: 0.5529 (mp10) cc_final: 0.5226 (mm-40) REVERT: B 57 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8567 (tt) REVERT: B 87 LYS cc_start: 0.8030 (tptt) cc_final: 0.7526 (tptt) REVERT: B 201 LEU cc_start: 0.8350 (tp) cc_final: 0.7994 (mt) REVERT: B 203 ARG cc_start: 0.7435 (tpt170) cc_final: 0.6829 (tpt170) REVERT: B 217 LEU cc_start: 0.8460 (mt) cc_final: 0.8062 (mt) REVERT: B 296 LEU cc_start: 0.8644 (mt) cc_final: 0.8248 (tp) REVERT: B 319 ARG cc_start: 0.7667 (mmp-170) cc_final: 0.7446 (tpp80) REVERT: B 710 GLU cc_start: 0.6146 (tp30) cc_final: 0.5824 (tp30) REVERT: C 57 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8676 (mm) REVERT: C 211 ASN cc_start: 0.8097 (m-40) cc_final: 0.7493 (m110) REVERT: C 215 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8429 (mm-30) REVERT: E 6 GLU cc_start: 0.7057 (pp20) cc_final: 0.6668 (mm-30) REVERT: E 231 LEU cc_start: 0.8119 (tp) cc_final: 0.7908 (mt) REVERT: E 309 TYR cc_start: 0.8391 (m-80) cc_final: 0.7633 (m-80) REVERT: E 310 LEU cc_start: 0.8036 (tp) cc_final: 0.7675 (tt) REVERT: E 383 ARG cc_start: 0.7405 (ttt90) cc_final: 0.6982 (ttm-80) REVERT: E 472 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: E 549 LEU cc_start: 0.8433 (mm) cc_final: 0.8115 (mm) outliers start: 65 outliers final: 44 residues processed: 277 average time/residue: 0.2008 time to fit residues: 87.1230 Evaluate side-chains 242 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 109 optimal weight: 0.6980 chunk 314 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 344 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.190836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.150742 restraints weight = 48777.406| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 4.57 r_work: 0.3638 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28447 Z= 0.117 Angle : 0.554 11.408 38623 Z= 0.275 Chirality : 0.039 0.149 4305 Planarity : 0.004 0.048 5155 Dihedral : 4.102 42.249 4002 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.36 % Allowed : 12.22 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.14), residues: 3585 helix: 1.68 (0.12), residues: 1859 sheet: -0.03 (0.26), residues: 399 loop : -0.39 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 139 TYR 0.020 0.002 TYR B 271 PHE 0.013 0.001 PHE C 119 TRP 0.039 0.002 TRP A 403 HIS 0.005 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00256 (28447) covalent geometry : angle 0.55421 (38623) hydrogen bonds : bond 0.03731 ( 1550) hydrogen bonds : angle 4.41729 ( 4506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.2428 (mt) cc_final: 0.1883 (mt) REVERT: A 193 GLU cc_start: 0.4728 (tt0) cc_final: 0.3971 (mm-30) REVERT: A 205 TRP cc_start: 0.6661 (t-100) cc_final: 0.6141 (t-100) REVERT: A 217 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7846 (mm) REVERT: A 416 LEU cc_start: 0.7488 (tt) cc_final: 0.7232 (tt) REVERT: A 426 MET cc_start: 0.7177 (mtp) cc_final: 0.6923 (mtm) REVERT: A 534 GLU cc_start: 0.5683 (mp0) cc_final: 0.5029 (mt-10) REVERT: A 558 ILE cc_start: 0.4504 (OUTLIER) cc_final: 0.3851 (tp) REVERT: A 623 ASN cc_start: 0.6963 (p0) cc_final: 0.6564 (p0) REVERT: B 57 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8318 (tt) REVERT: B 201 LEU cc_start: 0.8393 (tp) cc_final: 0.8044 (mt) REVERT: B 217 LEU cc_start: 0.8541 (mt) cc_final: 0.8129 (mt) REVERT: B 280 ARG cc_start: 0.7419 (tmm-80) cc_final: 0.7027 (ttp80) REVERT: B 282 ASP cc_start: 0.7669 (t0) cc_final: 0.7301 (t0) REVERT: B 283 TYR cc_start: 0.6837 (m-80) cc_final: 0.6413 (m-80) REVERT: B 296 LEU cc_start: 0.8558 (mt) cc_final: 0.7981 (tp) REVERT: B 385 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6904 (mm-30) REVERT: B 650 ASN cc_start: 0.8206 (m-40) cc_final: 0.7948 (t0) REVERT: C 211 ASN cc_start: 0.8058 (m-40) cc_final: 0.7441 (m110) REVERT: C 215 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8539 (mm-30) REVERT: C 327 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7296 (ttpt) REVERT: D 386 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: E 6 GLU cc_start: 0.7106 (pp20) cc_final: 0.6633 (mm-30) REVERT: E 205 TRP cc_start: 0.7859 (m100) cc_final: 0.7474 (t-100) REVERT: E 231 LEU cc_start: 0.8095 (tp) cc_final: 0.7881 (mt) REVERT: E 309 TYR cc_start: 0.8444 (m-80) cc_final: 0.7950 (m-80) REVERT: E 310 LEU cc_start: 0.8037 (tp) cc_final: 0.7795 (tt) REVERT: E 383 ARG cc_start: 0.7354 (ttt90) cc_final: 0.6853 (ttm-80) REVERT: E 385 GLU cc_start: 0.6441 (mt-10) cc_final: 0.5909 (tt0) REVERT: E 549 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8178 (mm) REVERT: E 612 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6047 (pp30) outliers start: 67 outliers final: 39 residues processed: 273 average time/residue: 0.1806 time to fit residues: 80.8455 Evaluate side-chains 244 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 90 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 316 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.186769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.136402 restraints weight = 49395.107| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.23 r_work: 0.3578 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28447 Z= 0.273 Angle : 0.651 12.006 38623 Z= 0.325 Chirality : 0.042 0.166 4305 Planarity : 0.005 0.066 5155 Dihedral : 4.330 44.323 4002 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.43 % Allowed : 12.71 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.82 (0.14), residues: 3585 helix: 1.52 (0.12), residues: 1863 sheet: -0.34 (0.26), residues: 410 loop : -0.51 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 200 TYR 0.026 0.002 TYR C 50 PHE 0.026 0.002 PHE A 630 TRP 0.038 0.002 TRP A 403 HIS 0.010 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00638 (28447) covalent geometry : angle 0.65070 (38623) hydrogen bonds : bond 0.04092 ( 1550) hydrogen bonds : angle 4.69753 ( 4506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.4879 (tt0) cc_final: 0.4023 (mm-30) REVERT: A 205 TRP cc_start: 0.6690 (t-100) cc_final: 0.6140 (t-100) REVERT: A 416 LEU cc_start: 0.7483 (tt) cc_final: 0.7193 (tt) REVERT: A 426 MET cc_start: 0.7270 (mtp) cc_final: 0.6970 (mtm) REVERT: A 534 GLU cc_start: 0.5850 (mp0) cc_final: 0.5266 (mt-10) REVERT: A 558 ILE cc_start: 0.4616 (OUTLIER) cc_final: 0.3995 (tp) REVERT: A 623 ASN cc_start: 0.7266 (p0) cc_final: 0.6889 (p0) REVERT: A 642 GLN cc_start: 0.5646 (mp10) cc_final: 0.5255 (mm-40) REVERT: B 57 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 201 LEU cc_start: 0.8425 (tp) cc_final: 0.8044 (mt) REVERT: B 203 ARG cc_start: 0.7550 (tpt170) cc_final: 0.6892 (tpt170) REVERT: B 217 LEU cc_start: 0.8598 (mt) cc_final: 0.8153 (mt) REVERT: B 296 LEU cc_start: 0.8682 (mt) cc_final: 0.8189 (tp) REVERT: B 319 ARG cc_start: 0.7808 (mmp-170) cc_final: 0.7450 (tpp80) REVERT: B 385 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7127 (mm-30) REVERT: B 710 GLU cc_start: 0.5862 (tp30) cc_final: 0.5469 (tp30) REVERT: C 57 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8685 (mm) REVERT: C 211 ASN cc_start: 0.8229 (m-40) cc_final: 0.7541 (m110) REVERT: C 215 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 327 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7458 (ttpt) REVERT: D 135 PHE cc_start: 0.4588 (m-10) cc_final: 0.4063 (m-10) REVERT: E 6 GLU cc_start: 0.7177 (pp20) cc_final: 0.6644 (mm-30) REVERT: E 231 LEU cc_start: 0.8213 (tp) cc_final: 0.7985 (mt) REVERT: E 309 TYR cc_start: 0.8594 (m-80) cc_final: 0.8002 (m-80) REVERT: E 310 LEU cc_start: 0.8092 (tp) cc_final: 0.7831 (tt) REVERT: E 383 ARG cc_start: 0.7568 (ttt90) cc_final: 0.7262 (ttm-80) REVERT: E 472 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6796 (m-10) REVERT: E 549 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8211 (mm) outliers start: 69 outliers final: 50 residues processed: 260 average time/residue: 0.1835 time to fit residues: 77.3557 Evaluate side-chains 252 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 0 optimal weight: 10.0000 chunk 354 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 281 optimal weight: 0.6980 chunk 278 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 25 optimal weight: 40.0000 chunk 292 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.190967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.153878 restraints weight = 49018.185| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.80 r_work: 0.3595 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28447 Z= 0.115 Angle : 0.555 13.259 38623 Z= 0.272 Chirality : 0.039 0.183 4305 Planarity : 0.004 0.044 5155 Dihedral : 4.068 42.817 4002 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.01 % Allowed : 13.66 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.14), residues: 3585 helix: 1.74 (0.12), residues: 1860 sheet: -0.09 (0.26), residues: 408 loop : -0.42 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 657 TYR 0.016 0.002 TYR C 557 PHE 0.014 0.001 PHE C 124 TRP 0.045 0.002 TRP A 403 HIS 0.011 0.001 HIS B 527 Details of bonding type rmsd covalent geometry : bond 0.00255 (28447) covalent geometry : angle 0.55467 (38623) hydrogen bonds : bond 0.03596 ( 1550) hydrogen bonds : angle 4.34638 ( 4506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7444 (mm) cc_final: 0.6584 (tt) REVERT: A 193 GLU cc_start: 0.4457 (tt0) cc_final: 0.3793 (mm-30) REVERT: A 205 TRP cc_start: 0.6754 (t-100) cc_final: 0.6194 (t-100) REVERT: A 416 LEU cc_start: 0.7435 (tt) cc_final: 0.7165 (tt) REVERT: A 426 MET cc_start: 0.7175 (mtp) cc_final: 0.6947 (mtm) REVERT: A 534 GLU cc_start: 0.5716 (mp0) cc_final: 0.5060 (mt-10) REVERT: A 558 ILE cc_start: 0.4521 (OUTLIER) cc_final: 0.3882 (tp) REVERT: A 623 ASN cc_start: 0.7051 (p0) cc_final: 0.6693 (p0) REVERT: B 57 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8257 (tt) REVERT: B 87 LYS cc_start: 0.8201 (tptt) cc_final: 0.7831 (mttm) REVERT: B 201 LEU cc_start: 0.8351 (tp) cc_final: 0.8011 (mt) REVERT: B 217 LEU cc_start: 0.8526 (mt) cc_final: 0.8099 (mp) REVERT: B 282 ASP cc_start: 0.7568 (t0) cc_final: 0.7037 (t0) REVERT: B 296 LEU cc_start: 0.8612 (mt) cc_final: 0.8107 (tp) REVERT: B 385 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7042 (mm-30) REVERT: B 532 ASP cc_start: 0.6141 (t70) cc_final: 0.5595 (t70) REVERT: B 650 ASN cc_start: 0.8170 (m-40) cc_final: 0.7964 (t0) REVERT: C 132 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7433 (pp20) REVERT: C 211 ASN cc_start: 0.8085 (m-40) cc_final: 0.7501 (m110) REVERT: C 327 LYS cc_start: 0.7602 (ttpt) cc_final: 0.7344 (ttpt) REVERT: C 696 GLN cc_start: 0.7573 (tp40) cc_final: 0.7329 (tp40) REVERT: D 365 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7425 (mm-30) REVERT: D 386 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: E 205 TRP cc_start: 0.7770 (m100) cc_final: 0.7244 (t-100) REVERT: E 309 TYR cc_start: 0.8496 (m-80) cc_final: 0.8089 (m-80) REVERT: E 383 ARG cc_start: 0.7405 (ttt90) cc_final: 0.6901 (ttm-80) REVERT: E 385 GLU cc_start: 0.6449 (mt-10) cc_final: 0.5875 (tt0) REVERT: E 472 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6617 (m-10) REVERT: E 549 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8133 (mm) outliers start: 57 outliers final: 41 residues processed: 260 average time/residue: 0.1752 time to fit residues: 75.1720 Evaluate side-chains 236 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 277 optimal weight: 0.9980 chunk 328 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS ** E 650 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 = 0.4514 r_free = 0.4514 target = 0.190017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152233 restraints weight = 49058.919| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.81 r_work: 0.3580 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28447 Z= 0.148 Angle : 0.560 12.849 38623 Z= 0.276 Chirality : 0.039 0.252 4305 Planarity : 0.004 0.043 5155 Dihedral : 4.038 43.976 4002 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.25 % Allowed : 14.05 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.14), residues: 3585 helix: 1.75 (0.12), residues: 1874 sheet: -0.15 (0.26), residues: 429 loop : -0.37 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 688 TYR 0.017 0.002 TYR C 50 PHE 0.018 0.001 PHE C 135 TRP 0.042 0.002 TRP A 403 HIS 0.005 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00343 (28447) covalent geometry : angle 0.56043 (38623) hydrogen bonds : bond 0.03599 ( 1550) hydrogen bonds : angle 4.36899 ( 4506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7554 (mm) cc_final: 0.6648 (tt) REVERT: A 193 GLU cc_start: 0.4564 (tt0) cc_final: 0.3851 (mm-30) REVERT: A 205 TRP cc_start: 0.6703 (t-100) cc_final: 0.6147 (t-100) REVERT: A 416 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7184 (tt) REVERT: A 534 GLU cc_start: 0.5752 (mp0) cc_final: 0.5082 (mt-10) REVERT: A 558 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.3956 (tp) REVERT: A 623 ASN cc_start: 0.7074 (p0) cc_final: 0.6718 (p0) REVERT: A 642 GLN cc_start: 0.5369 (mp10) cc_final: 0.5063 (mm-40) REVERT: B 57 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 87 LYS cc_start: 0.8187 (tptt) cc_final: 0.7828 (mttm) REVERT: B 201 LEU cc_start: 0.8326 (tp) cc_final: 0.7978 (mt) REVERT: B 217 LEU cc_start: 0.8529 (mt) cc_final: 0.8079 (mp) REVERT: B 282 ASP cc_start: 0.7569 (t0) cc_final: 0.7170 (t0) REVERT: B 296 LEU cc_start: 0.8648 (mt) cc_final: 0.8111 (tp) REVERT: B 385 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7074 (mm-30) REVERT: B 650 ASN cc_start: 0.8223 (m-40) cc_final: 0.8013 (t0) REVERT: C 57 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8613 (mm) REVERT: C 132 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: C 211 ASN cc_start: 0.8031 (m-40) cc_final: 0.7636 (m110) REVERT: C 327 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7408 (ttpt) REVERT: D 135 PHE cc_start: 0.4588 (m-10) cc_final: 0.4087 (m-10) REVERT: D 194 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 386 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: E 205 TRP cc_start: 0.7840 (m100) cc_final: 0.7462 (t-100) REVERT: E 309 TYR cc_start: 0.8480 (m-80) cc_final: 0.8169 (m-80) REVERT: E 383 ARG cc_start: 0.7426 (ttt90) cc_final: 0.7185 (ttm-80) REVERT: E 472 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6716 (m-10) REVERT: E 549 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8152 (mm) outliers start: 64 outliers final: 46 residues processed: 249 average time/residue: 0.1734 time to fit residues: 71.2432 Evaluate side-chains 243 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 258 optimal weight: 0.0070 chunk 278 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 103 optimal weight: 0.0870 chunk 284 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS ** E 650 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 = 0.4530 r_free = 0.4530 target = 0.191582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.153012 restraints weight = 48995.161| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.58 r_work: 0.3632 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28447 Z= 0.119 Angle : 0.548 14.174 38623 Z= 0.268 Chirality : 0.039 0.256 4305 Planarity : 0.004 0.042 5155 Dihedral : 3.968 43.398 4002 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 14.12 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.14), residues: 3585 helix: 1.83 (0.12), residues: 1866 sheet: -0.14 (0.25), residues: 445 loop : -0.31 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 688 TYR 0.015 0.001 TYR C 557 PHE 0.015 0.001 PHE C 135 TRP 0.053 0.002 TRP A 403 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00270 (28447) covalent geometry : angle 0.54788 (38623) hydrogen bonds : bond 0.03477 ( 1550) hydrogen bonds : angle 4.28538 ( 4506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7516 (mm) cc_final: 0.6615 (tt) REVERT: A 118 LEU cc_start: 0.2705 (mt) cc_final: 0.2353 (mt) REVERT: A 193 GLU cc_start: 0.4416 (tt0) cc_final: 0.3772 (mm-30) REVERT: A 205 TRP cc_start: 0.6669 (t-100) cc_final: 0.6235 (t-100) REVERT: A 416 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7143 (tt) REVERT: A 494 ARG cc_start: 0.7052 (mtt90) cc_final: 0.6817 (ppt170) REVERT: A 534 GLU cc_start: 0.5655 (mp0) cc_final: 0.5008 (mt-10) REVERT: A 558 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.3991 (tp) REVERT: A 623 ASN cc_start: 0.7014 (p0) cc_final: 0.6694 (p0) REVERT: B 57 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8294 (tt) REVERT: B 87 LYS cc_start: 0.8208 (tptt) cc_final: 0.7863 (mttm) REVERT: B 201 LEU cc_start: 0.8311 (tp) cc_final: 0.7970 (mt) REVERT: B 217 LEU cc_start: 0.8478 (mt) cc_final: 0.8039 (mp) REVERT: B 282 ASP cc_start: 0.7461 (t0) cc_final: 0.6948 (t0) REVERT: B 296 LEU cc_start: 0.8608 (mt) cc_final: 0.8140 (tp) REVERT: B 385 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7041 (mm-30) REVERT: B 650 ASN cc_start: 0.8115 (m-40) cc_final: 0.7897 (t0) REVERT: C 132 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7340 (pp20) REVERT: C 211 ASN cc_start: 0.8002 (m-40) cc_final: 0.7633 (m110) REVERT: C 319 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7506 (mtm110) REVERT: C 327 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7336 (ttpt) REVERT: C 696 GLN cc_start: 0.7611 (tp40) cc_final: 0.7363 (tp40) REVERT: D 194 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7772 (tp) REVERT: D 219 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6589 (mt0) REVERT: E 103 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: E 205 TRP cc_start: 0.7769 (m100) cc_final: 0.7384 (t-100) REVERT: E 309 TYR cc_start: 0.8400 (m-80) cc_final: 0.8156 (m-80) REVERT: E 383 ARG cc_start: 0.7346 (ttt90) cc_final: 0.6896 (ttm-80) REVERT: E 385 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5880 (tt0) REVERT: E 472 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6584 (m-10) REVERT: E 549 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8142 (mm) outliers start: 58 outliers final: 48 residues processed: 253 average time/residue: 0.1798 time to fit residues: 73.5594 Evaluate side-chains 252 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 90 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 327 optimal weight: 0.0050 chunk 354 optimal weight: 30.0000 chunk 346 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 270 optimal weight: 0.9990 chunk 160 optimal weight: 20.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS ** E 650 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 = 0.4486 r_free = 0.4486 target = 0.187321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.141987 restraints weight = 49307.417| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.83 r_work: 0.3595 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 28447 Z= 0.248 Angle : 0.650 13.775 38623 Z= 0.323 Chirality : 0.042 0.266 4305 Planarity : 0.005 0.070 5155 Dihedral : 4.241 44.352 4002 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 14.19 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 3585 helix: 1.67 (0.12), residues: 1858 sheet: -0.40 (0.25), residues: 445 loop : -0.44 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 688 TYR 0.022 0.002 TYR C 50 PHE 0.035 0.002 PHE E 542 TRP 0.049 0.003 TRP A 403 HIS 0.013 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00581 (28447) covalent geometry : angle 0.65030 (38623) hydrogen bonds : bond 0.03867 ( 1550) hydrogen bonds : angle 4.59774 ( 4506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 197 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.2786 (mt) cc_final: 0.2369 (mt) REVERT: A 193 GLU cc_start: 0.4680 (tt0) cc_final: 0.3900 (mm-30) REVERT: A 205 TRP cc_start: 0.6670 (t-100) cc_final: 0.6186 (t-100) REVERT: A 416 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7184 (tt) REVERT: A 534 GLU cc_start: 0.5878 (mp0) cc_final: 0.5191 (mt-10) REVERT: A 558 ILE cc_start: 0.4681 (OUTLIER) cc_final: 0.4050 (tp) REVERT: A 623 ASN cc_start: 0.7235 (p0) cc_final: 0.6911 (p0) REVERT: A 689 MET cc_start: 0.1330 (mmt) cc_final: 0.0956 (tpt) REVERT: B 57 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 87 LYS cc_start: 0.8261 (tptt) cc_final: 0.7927 (mttm) REVERT: B 201 LEU cc_start: 0.8403 (tp) cc_final: 0.8004 (mt) REVERT: B 231 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (tt) REVERT: B 232 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7707 (ptm-80) REVERT: B 280 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7108 (ttp80) REVERT: B 385 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7163 (mm-30) REVERT: C 57 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8648 (mm) REVERT: C 211 ASN cc_start: 0.8117 (m-40) cc_final: 0.7702 (m110) REVERT: C 327 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7522 (ttpt) REVERT: C 603 ASP cc_start: 0.7621 (m-30) cc_final: 0.7169 (m-30) REVERT: E 103 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: E 205 TRP cc_start: 0.7971 (m100) cc_final: 0.7600 (t-100) REVERT: E 309 TYR cc_start: 0.8543 (m-80) cc_final: 0.8085 (m-80) REVERT: E 383 ARG cc_start: 0.7577 (ttt90) cc_final: 0.7248 (ttm-80) REVERT: E 472 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: E 549 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8247 (mm) outliers start: 69 outliers final: 50 residues processed: 248 average time/residue: 0.1789 time to fit residues: 72.0794 Evaluate side-chains 243 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 612 GLN Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 16 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 272 optimal weight: 0.0570 chunk 306 optimal weight: 10.0000 chunk 341 optimal weight: 0.0170 chunk 186 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS ** E 650 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 = 0.4529 r_free = 0.4529 target = 0.191453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152471 restraints weight = 48745.253| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.92 r_work: 0.3635 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28447 Z= 0.113 Angle : 0.564 14.626 38623 Z= 0.275 Chirality : 0.039 0.257 4305 Planarity : 0.004 0.042 5155 Dihedral : 4.017 43.316 4002 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.90 % Allowed : 14.75 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.14), residues: 3585 helix: 1.82 (0.12), residues: 1860 sheet: -0.16 (0.25), residues: 443 loop : -0.35 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 688 TYR 0.017 0.002 TYR D 552 PHE 0.024 0.001 PHE C 119 TRP 0.056 0.002 TRP A 403 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00252 (28447) covalent geometry : angle 0.56357 (38623) hydrogen bonds : bond 0.03477 ( 1550) hydrogen bonds : angle 4.27541 ( 4506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7764.57 seconds wall clock time: 133 minutes 11.20 seconds (7991.20 seconds total)