Starting phenix.real_space_refine on Mon May 26 06:13:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k90_36970/05_2025/8k90_36970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k90_36970/05_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_36970/05_2025/8k90_36970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k90_36970/05_2025/8k90_36970.map" model { file = "/net/cci-nas-00/data/ceres_data/8k90_36970/05_2025/8k90_36970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k90_36970/05_2025/8k90_36970.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.02, per 1000 atoms: 0.57 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: 7.76 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 4.05 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: 11.39 Time building geometry restraints manager: 8.88 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: 0.06 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: 2.040 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: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 63.210 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (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 TRP 0.024 0.002 TRP C 205 HIS 0.006 0.001 HIS C 303 PHE 0.019 0.001 PHE B 629 TYR 0.023 0.002 TYR C 50 ARG 0.017 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.13973 ( 1550) hydrogen bonds : angle 5.97902 ( 4506) covalent geometry : bond 0.00542 (28447) covalent geometry : angle 0.73661 (38623) *********************** 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 : 3.728 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 193 GLU cc_start: 0.5332 (tt0) cc_final: 0.4881 (mm-30) REVERT: A 200 ARG cc_start: 0.7593 (tpp-160) cc_final: 0.7338 (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: 0.3777 (tpt170) REVERT: A 276 ARG cc_start: 0.6735 (mtp180) cc_final: 0.6453 (mmt90) REVERT: A 303 HIS cc_start: 0.7220 (m-70) cc_final: 0.6580 (m-70) REVERT: A 356 MET cc_start: 0.6603 (mpp) cc_final: 0.6214 (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: 0.7957 (mp) REVERT: B 203 ARG cc_start: 0.7246 (tpt170) cc_final: 0.6656 (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 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: 0.7661 (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: 0.6817 (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: 0.6795 (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: 0.6362 (tp) REVERT: E 179 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7354 (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) outliers start: 4 outliers final: 1 residues processed: 488 average time/residue: 0.4734 time to fit residues: 347.3021 Evaluate side-chains 265 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 299 optimal weight: 50.0000 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.190886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.137122 restraints weight = 48707.497| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.97 r_work: 0.3605 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28447 Z= 0.137 Angle : 0.586 8.547 38623 Z= 0.297 Chirality : 0.040 0.209 4305 Planarity : 0.005 0.063 5155 Dihedral : 4.153 44.234 4002 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.23 % Allowed : 7.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3585 helix: 1.73 (0.12), residues: 1852 sheet: 0.09 (0.26), residues: 422 loop : -0.33 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 250 HIS 0.006 0.001 HIS E 469 PHE 0.021 0.002 PHE C 119 TYR 0.020 0.002 TYR A 420 ARG 0.008 0.000 ARG E 688 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 1550) hydrogen bonds : angle 4.75118 ( 4506) covalent geometry : bond 0.00304 (28447) covalent geometry : angle 0.58641 (38623) *********************** 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 350 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 315 time to evaluate : 3.331 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 29 PHE cc_start: 0.5074 (m-80) cc_final: 0.3894 (m-10) REVERT: A 36 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7850 (ttm110) REVERT: A 64 LEU cc_start: 0.7439 (mm) cc_final: 0.6727 (tt) REVERT: A 118 LEU cc_start: 0.3312 (OUTLIER) cc_final: 0.2753 (mt) REVERT: A 128 LYS cc_start: 0.2544 (mmtm) cc_final: 0.2051 (mmtt) REVERT: A 193 GLU cc_start: 0.4909 (tt0) cc_final: 0.4246 (mm-30) REVERT: A 200 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7262 (ptt90) REVERT: A 276 ARG cc_start: 0.6513 (mtp180) cc_final: 0.6292 (mmt90) REVERT: A 303 HIS cc_start: 0.7457 (m-70) cc_final: 0.6853 (m170) REVERT: A 426 MET cc_start: 0.7176 (mtm) cc_final: 0.6883 (mtm) REVERT: A 534 GLU cc_start: 0.5900 (mp0) cc_final: 0.4991 (mt-10) REVERT: A 574 ASN cc_start: 0.6663 (p0) cc_final: 0.5917 (t0) REVERT: B 37 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7402 (pt0) REVERT: B 87 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8084 (tptt) REVERT: B 201 LEU cc_start: 0.8441 (tp) cc_final: 0.8125 (mt) REVERT: B 215 GLU cc_start: 0.9235 (pt0) cc_final: 0.9029 (pt0) REVERT: B 217 LEU cc_start: 0.8536 (mt) cc_final: 0.8098 (mt) REVERT: B 231 LEU cc_start: 0.8992 (tp) cc_final: 0.8789 (tt) REVERT: B 232 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7971 (tmm-80) REVERT: B 280 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6360 (ttp-110) REVERT: B 334 GLN cc_start: 0.8249 (mt0) cc_final: 0.8014 (mp-120) REVERT: B 348 GLU cc_start: 0.8012 (tt0) cc_final: 0.7246 (tp30) REVERT: B 382 ILE cc_start: 0.7920 (mm) cc_final: 0.7686 (mm) REVERT: C 211 ASN cc_start: 0.8295 (m-40) cc_final: 0.7668 (m110) REVERT: C 215 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8783 (mm-30) REVERT: C 269 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7845 (mm-30) REVERT: C 271 TYR cc_start: 0.7278 (t80) cc_final: 0.6971 (t80) REVERT: C 319 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7801 (ttp80) REVERT: C 334 GLN cc_start: 0.8296 (mt0) cc_final: 0.8040 (mt0) REVERT: C 342 GLN cc_start: 0.7364 (pt0) cc_final: 0.7087 (mp10) REVERT: C 395 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7917 (tp30) REVERT: C 405 LEU cc_start: 0.8421 (tp) cc_final: 0.8173 (mm) REVERT: C 494 ARG cc_start: 0.8848 (mtt-85) cc_final: 0.8611 (mtt-85) REVERT: C 579 GLU cc_start: 0.5336 (mp0) cc_final: 0.4950 (pm20) REVERT: C 683 ILE cc_start: 0.8437 (mt) cc_final: 0.8213 (mt) REVERT: D 219 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6797 (mt0) REVERT: D 454 LEU cc_start: 0.8368 (tt) cc_final: 0.7847 (mm) REVERT: E 6 GLU cc_start: 0.7046 (pp20) cc_final: 0.6559 (mm-30) REVERT: E 52 VAL cc_start: 0.8685 (t) cc_final: 0.8411 (t) REVERT: E 103 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: E 205 TRP cc_start: 0.8016 (m100) cc_final: 0.7265 (m-10) REVERT: E 231 LEU cc_start: 0.8194 (tp) cc_final: 0.7985 (mt) REVERT: E 241 THR cc_start: 0.7306 (m) cc_final: 0.7075 (m) REVERT: E 323 TRP cc_start: 0.7860 (t-100) cc_final: 0.7527 (t-100) REVERT: E 348 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8268 (tt0) REVERT: E 368 GLU cc_start: 0.5254 (mm-30) cc_final: 0.4890 (mt-10) REVERT: E 383 ARG cc_start: 0.7116 (ttt90) cc_final: 0.6510 (ttm-80) REVERT: E 385 GLU cc_start: 0.6478 (mt-10) cc_final: 0.5665 (tt0) REVERT: E 475 GLU cc_start: 0.4934 (mm-30) cc_final: 0.4678 (mp0) outliers start: 35 outliers final: 26 residues processed: 339 average time/residue: 0.4258 time to fit residues: 223.5413 Evaluate side-chains 273 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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 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 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 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 79 optimal weight: 0.0370 chunk 4 optimal weight: 20.0000 chunk 335 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 chunk 241 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 overall best weight: 1.1458 ------------------------------------------------------------------------------- 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 C 696 GLN ** 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 = 0.4539 r_free = 0.4539 target = 0.192769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.155834 restraints weight = 49043.953| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.61 r_work: 0.3635 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28447 Z= 0.132 Angle : 0.544 9.029 38623 Z= 0.274 Chirality : 0.039 0.173 4305 Planarity : 0.004 0.050 5155 Dihedral : 4.024 44.816 4002 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.41 % Allowed : 9.51 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3585 helix: 1.72 (0.12), residues: 1863 sheet: 0.08 (0.26), residues: 422 loop : -0.28 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 403 HIS 0.007 0.001 HIS A 208 PHE 0.014 0.001 PHE B 629 TYR 0.022 0.002 TYR B 271 ARG 0.012 0.000 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 1550) hydrogen bonds : angle 4.52254 ( 4506) covalent geometry : bond 0.00296 (28447) covalent geometry : angle 0.54380 (38623) *********************** 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: 40 poor density : 270 time to evaluate : 2.973 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: 0.7524 (mm) cc_final: 0.6634 (tt) REVERT: A 193 GLU cc_start: 0.4680 (tt0) cc_final: 0.4035 (mm-30) REVERT: A 205 TRP cc_start: 0.6736 (t-100) cc_final: 0.6273 (t-100) REVERT: A 276 ARG cc_start: 0.6562 (mtp180) cc_final: 0.6338 (mmt90) REVERT: A 303 HIS cc_start: 0.7122 (m-70) cc_final: 0.6745 (m170) REVERT: A 534 GLU cc_start: 0.5593 (mp0) cc_final: 0.4838 (mt-10) REVERT: A 574 ASN cc_start: 0.6629 (p0) cc_final: 0.6032 (t0) REVERT: A 623 ASN cc_start: 0.6658 (p0) cc_final: 0.6160 (p0) REVERT: B 57 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 201 LEU cc_start: 0.8423 (tp) cc_final: 0.8084 (mt) REVERT: B 215 GLU cc_start: 0.9079 (pt0) cc_final: 0.8842 (pt0) REVERT: B 217 LEU cc_start: 0.8457 (mt) cc_final: 0.8076 (mt) REVERT: B 296 LEU cc_start: 0.8520 (mt) cc_final: 0.7996 (tp) REVERT: B 348 GLU cc_start: 0.7817 (tt0) cc_final: 0.7344 (tp30) REVERT: C 132 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: C 211 ASN cc_start: 0.8068 (m-40) cc_final: 0.7467 (m110) REVERT: C 215 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8546 (mm-30) REVERT: C 269 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 405 LEU cc_start: 0.8493 (tp) cc_final: 0.8251 (mm) REVERT: C 683 ILE cc_start: 0.8390 (mt) cc_final: 0.8179 (mt) REVERT: D 219 GLN cc_start: 0.7253 (mm-40) cc_final: 0.7005 (mm-40) REVERT: E 6 GLU cc_start: 0.7017 (pp20) cc_final: 0.6635 (mm-30) REVERT: E 103 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: E 205 TRP cc_start: 0.7815 (m100) cc_final: 0.7113 (m-10) REVERT: E 383 ARG cc_start: 0.7289 (ttt90) cc_final: 0.6854 (ttm-80) REVERT: E 385 GLU cc_start: 0.6488 (mt-10) cc_final: 0.5936 (tt0) REVERT: E 472 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6347 (m-10) REVERT: E 549 LEU cc_start: 0.8408 (mm) cc_final: 0.8095 (mm) outliers start: 40 outliers final: 27 residues processed: 295 average time/residue: 0.4127 time to fit residues: 190.0679 Evaluate side-chains 239 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 2.943 ------------------------------------------------------------------------------- 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 461 GLU Chi-restraints excluded: chain A residue 674 VAL 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 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 496 VAL Chi-restraints excluded: chain D residue 503 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 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 630 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 343 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 314 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS 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 602 GLN C 612 GLN C 696 GLN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.186278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.147999 restraints weight = 49319.436| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 4.50 r_work: 0.3535 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 28447 Z= 0.323 Angle : 0.715 10.174 38623 Z= 0.362 Chirality : 0.044 0.163 4305 Planarity : 0.006 0.072 5155 Dihedral : 4.502 44.832 4002 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.85 % Allowed : 10.95 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3585 helix: 1.32 (0.12), residues: 1864 sheet: -0.31 (0.26), residues: 422 loop : -0.61 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 403 HIS 0.016 0.002 HIS C 303 PHE 0.033 0.002 PHE A 630 TYR 0.032 0.003 TYR C 50 ARG 0.009 0.001 ARG B 298 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 1550) hydrogen bonds : angle 4.93527 ( 4506) covalent geometry : bond 0.00755 (28447) covalent geometry : angle 0.71493 (38623) *********************** 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 313 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 232 time to evaluate : 3.124 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 37 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: A 118 LEU cc_start: 0.2492 (mt) cc_final: 0.1947 (mt) REVERT: A 193 GLU cc_start: 0.4562 (tt0) cc_final: 0.3801 (mm-30) REVERT: A 205 TRP cc_start: 0.6763 (t-100) cc_final: 0.6256 (t-100) REVERT: A 217 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 413 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: A 416 LEU cc_start: 0.7371 (tt) cc_final: 0.7047 (tt) REVERT: A 534 GLU cc_start: 0.5751 (mp0) cc_final: 0.5166 (mt-10) REVERT: A 558 ILE cc_start: 0.4597 (OUTLIER) cc_final: 0.3916 (tp) REVERT: A 623 ASN cc_start: 0.7047 (p0) cc_final: 0.6637 (p0) REVERT: A 642 GLN cc_start: 0.5477 (mp10) cc_final: 0.5229 (mm-40) REVERT: B 57 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8552 (tt) REVERT: B 87 LYS cc_start: 0.8062 (tptt) cc_final: 0.7642 (tptt) REVERT: B 201 LEU cc_start: 0.8341 (tp) cc_final: 0.7988 (mt) REVERT: B 203 ARG cc_start: 0.7411 (tpt170) cc_final: 0.6799 (tpt170) REVERT: B 215 GLU cc_start: 0.9012 (pt0) cc_final: 0.8761 (pt0) REVERT: B 296 LEU cc_start: 0.8791 (mt) cc_final: 0.8419 (tp) REVERT: B 319 ARG cc_start: 0.7716 (mmp-170) cc_final: 0.7466 (tpp80) REVERT: B 348 GLU cc_start: 0.7761 (tt0) cc_final: 0.7529 (tp30) REVERT: B 527 HIS cc_start: 0.6381 (t-90) cc_final: 0.6037 (t70) REVERT: B 710 GLU cc_start: 0.6045 (tp30) cc_final: 0.5724 (tp30) REVERT: C 57 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8652 (mm) REVERT: C 211 ASN cc_start: 0.8078 (m-40) cc_final: 0.7488 (m110) REVERT: C 215 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8542 (mm-30) REVERT: C 603 ASP cc_start: 0.7540 (m-30) cc_final: 0.6911 (m-30) REVERT: E 309 TYR cc_start: 0.8510 (m-80) cc_final: 0.7813 (m-80) REVERT: E 310 LEU cc_start: 0.8107 (tp) cc_final: 0.7774 (tt) REVERT: E 383 ARG cc_start: 0.7507 (ttt90) cc_final: 0.7011 (ttm-80) REVERT: E 549 LEU cc_start: 0.8497 (mm) cc_final: 0.8172 (mm) outliers start: 81 outliers final: 46 residues processed: 293 average time/residue: 0.3891 time to fit residues: 181.1649 Evaluate side-chains 249 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 2.758 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 413 GLN 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 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 124 PHE 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 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 182 GLU Chi-restraints excluded: chain D residue 273 THR 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 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 194 LEU Chi-restraints excluded: chain E residue 397 CYS Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 546 VAL 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 201 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** 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 = 0.4497 r_free = 0.4497 target = 0.188464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.149624 restraints weight = 49052.994| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 4.01 r_work: 0.3571 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28447 Z= 0.200 Angle : 0.596 10.816 38623 Z= 0.299 Chirality : 0.040 0.171 4305 Planarity : 0.004 0.053 5155 Dihedral : 4.277 43.317 4002 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.61 % Allowed : 12.50 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3585 helix: 1.47 (0.12), residues: 1869 sheet: -0.30 (0.26), residues: 396 loop : -0.56 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 403 HIS 0.007 0.001 HIS C 303 PHE 0.021 0.002 PHE C 119 TYR 0.023 0.002 TYR C 50 ARG 0.005 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 1550) hydrogen bonds : angle 4.62694 ( 4506) covalent geometry : bond 0.00463 (28447) covalent geometry : angle 0.59556 (38623) *********************** 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 297 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 2.848 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: A 193 GLU cc_start: 0.4391 (tt0) cc_final: 0.3741 (mm-30) REVERT: A 205 TRP cc_start: 0.6729 (t-100) cc_final: 0.6149 (t-100) REVERT: A 217 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (mm) REVERT: A 413 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: A 416 LEU cc_start: 0.7432 (tt) cc_final: 0.7132 (tt) REVERT: A 426 MET cc_start: 0.7333 (mtp) cc_final: 0.7043 (mtm) REVERT: A 534 GLU cc_start: 0.5718 (mp0) cc_final: 0.5149 (mt-10) REVERT: A 558 ILE cc_start: 0.4580 (OUTLIER) cc_final: 0.3944 (tp) REVERT: A 623 ASN cc_start: 0.7125 (p0) cc_final: 0.6755 (p0) REVERT: A 642 GLN cc_start: 0.5311 (mp10) cc_final: 0.5093 (mm-40) REVERT: B 57 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8344 (tt) REVERT: B 87 LYS cc_start: 0.8046 (tptt) cc_final: 0.7673 (tptt) REVERT: B 201 LEU cc_start: 0.8341 (tp) cc_final: 0.7999 (mt) REVERT: B 215 GLU cc_start: 0.8967 (pt0) cc_final: 0.8721 (pt0) REVERT: B 282 ASP cc_start: 0.7695 (m-30) cc_final: 0.7201 (t0) REVERT: B 296 LEU cc_start: 0.8799 (mt) cc_final: 0.8302 (tp) REVERT: B 319 ARG cc_start: 0.7655 (mmp-170) cc_final: 0.7417 (tpp80) REVERT: B 348 GLU cc_start: 0.7802 (tt0) cc_final: 0.7584 (tp30) REVERT: B 710 GLU cc_start: 0.6077 (tp30) cc_final: 0.5783 (tp30) REVERT: C 211 ASN cc_start: 0.8079 (m-40) cc_final: 0.7442 (m110) REVERT: C 215 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8554 (mm-30) REVERT: C 327 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7348 (ttpt) REVERT: C 603 ASP cc_start: 0.7442 (m-30) cc_final: 0.6922 (m-30) REVERT: D 386 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: E 205 TRP cc_start: 0.7733 (m100) cc_final: 0.7331 (t-100) REVERT: E 309 TYR cc_start: 0.8547 (m-80) cc_final: 0.8084 (m-80) REVERT: E 310 LEU cc_start: 0.8198 (tp) cc_final: 0.7946 (tt) REVERT: E 383 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7004 (ttm-80) REVERT: E 385 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5979 (tt0) REVERT: E 472 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: E 549 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8142 (mm) outliers start: 74 outliers final: 51 residues processed: 277 average time/residue: 0.3883 time to fit residues: 173.3546 Evaluate side-chains 250 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 2.886 ------------------------------------------------------------------------------- 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 413 GLN 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 610 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 661 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 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 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 411 LEU 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 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 182 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 LEU 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 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 549 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 159 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 317 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.189566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.149546 restraints weight = 49048.994| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.76 r_work: 0.3604 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28447 Z= 0.160 Angle : 0.569 11.099 38623 Z= 0.283 Chirality : 0.039 0.228 4305 Planarity : 0.004 0.048 5155 Dihedral : 4.156 44.558 4002 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.71 % Allowed : 13.17 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3585 helix: 1.62 (0.12), residues: 1860 sheet: -0.31 (0.26), residues: 409 loop : -0.45 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 403 HIS 0.005 0.001 HIS C 303 PHE 0.016 0.002 PHE C 135 TYR 0.023 0.002 TYR B 227 ARG 0.014 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 1550) hydrogen bonds : angle 4.46246 ( 4506) covalent geometry : bond 0.00368 (28447) covalent geometry : angle 0.56935 (38623) *********************** 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 289 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 212 time to evaluate : 2.903 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 64 LEU cc_start: 0.7509 (mm) cc_final: 0.6632 (tt) REVERT: A 118 LEU cc_start: 0.2630 (mt) cc_final: 0.2165 (mt) REVERT: A 193 GLU cc_start: 0.4715 (tt0) cc_final: 0.3921 (mm-30) REVERT: A 205 TRP cc_start: 0.6674 (t-100) cc_final: 0.6134 (t-100) REVERT: A 217 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7844 (mm) REVERT: A 218 PHE cc_start: 0.4057 (m-80) cc_final: 0.3484 (m-80) REVERT: A 416 LEU cc_start: 0.7498 (tt) cc_final: 0.7231 (tt) REVERT: A 426 MET cc_start: 0.7131 (mtp) cc_final: 0.6897 (mtm) REVERT: A 534 GLU cc_start: 0.5828 (mp0) cc_final: 0.5168 (mt-10) REVERT: A 558 ILE cc_start: 0.4485 (OUTLIER) cc_final: 0.3864 (tp) REVERT: A 623 ASN cc_start: 0.7153 (p0) cc_final: 0.6750 (p0) REVERT: A 642 GLN cc_start: 0.5383 (mp10) cc_final: 0.5062 (mm-40) REVERT: B 57 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 87 LYS cc_start: 0.8082 (tptt) cc_final: 0.7745 (tptt) REVERT: B 201 LEU cc_start: 0.8409 (tp) cc_final: 0.8054 (mt) REVERT: B 215 GLU cc_start: 0.9049 (pt0) cc_final: 0.8820 (pt0) REVERT: B 348 GLU cc_start: 0.7820 (tt0) cc_final: 0.7562 (tp30) REVERT: C 57 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8621 (mm) REVERT: C 211 ASN cc_start: 0.8183 (m-40) cc_final: 0.7515 (m110) REVERT: C 327 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7340 (ttpt) REVERT: D 135 PHE cc_start: 0.4570 (m-10) cc_final: 0.4165 (m-10) REVERT: D 386 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: E 309 TYR cc_start: 0.8309 (m-80) cc_final: 0.7785 (m-80) REVERT: E 310 LEU cc_start: 0.8076 (tp) cc_final: 0.7847 (tt) REVERT: E 383 ARG cc_start: 0.7384 (ttt90) cc_final: 0.6893 (ttm-80) REVERT: E 385 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6011 (tt0) REVERT: E 472 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6533 (m-10) REVERT: E 549 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8173 (mm) outliers start: 77 outliers final: 53 residues processed: 273 average time/residue: 0.3520 time to fit residues: 159.1436 Evaluate side-chains 257 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 2.821 ------------------------------------------------------------------------------- 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 443 LEU 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 610 VAL Chi-restraints excluded: chain A residue 661 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 395 GLU Chi-restraints excluded: chain B residue 454 LEU 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 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 378 GLU Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 411 LEU 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 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 81 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 198 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 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 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 215 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 318 optimal weight: 6.9990 chunk 104 optimal weight: 0.0470 chunk 144 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 256 optimal weight: 0.7980 overall best weight: 2.7684 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** 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** D 679 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.187718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143050 restraints weight = 48870.599| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.79 r_work: 0.3614 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28447 Z= 0.213 Angle : 0.605 10.446 38623 Z= 0.301 Chirality : 0.040 0.170 4305 Planarity : 0.004 0.053 5155 Dihedral : 4.240 45.355 4002 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.57 % Allowed : 13.52 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3585 helix: 1.59 (0.12), residues: 1860 sheet: -0.26 (0.26), residues: 403 loop : -0.58 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 403 HIS 0.007 0.001 HIS C 303 PHE 0.021 0.002 PHE A 630 TYR 0.021 0.002 TYR C 50 ARG 0.005 0.000 ARG D 688 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1550) hydrogen bonds : angle 4.58161 ( 4506) covalent geometry : bond 0.00497 (28447) covalent geometry : angle 0.60484 (38623) *********************** 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: 73 poor density : 202 time to evaluate : 2.797 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 118 LEU cc_start: 0.2845 (mt) cc_final: 0.2427 (mt) REVERT: A 193 GLU cc_start: 0.4591 (tt0) cc_final: 0.3837 (mm-30) REVERT: A 205 TRP cc_start: 0.6711 (t-100) cc_final: 0.6164 (t-100) REVERT: A 217 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7747 (mm) REVERT: A 218 PHE cc_start: 0.4201 (m-80) cc_final: 0.3663 (m-80) REVERT: A 416 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7121 (tt) REVERT: A 426 MET cc_start: 0.7216 (mtp) cc_final: 0.6975 (mtm) REVERT: A 534 GLU cc_start: 0.5731 (mp0) cc_final: 0.5106 (mt-10) REVERT: A 558 ILE cc_start: 0.4570 (OUTLIER) cc_final: 0.3942 (tp) REVERT: A 623 ASN cc_start: 0.7182 (p0) cc_final: 0.6819 (p0) REVERT: B 57 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 87 LYS cc_start: 0.8111 (tptt) cc_final: 0.7689 (tptt) REVERT: B 201 LEU cc_start: 0.8307 (tp) cc_final: 0.7951 (mt) REVERT: B 203 ARG cc_start: 0.7519 (tpt170) cc_final: 0.6981 (tpt170) REVERT: B 215 GLU cc_start: 0.9006 (pt0) cc_final: 0.8780 (pt0) REVERT: B 282 ASP cc_start: 0.7347 (t0) cc_final: 0.7041 (t0) REVERT: B 296 LEU cc_start: 0.8738 (mt) cc_final: 0.8488 (tp) REVERT: B 319 ARG cc_start: 0.7691 (mmp-170) cc_final: 0.7400 (tpp80) REVERT: B 532 ASP cc_start: 0.6286 (t70) cc_final: 0.5825 (t70) REVERT: C 57 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8588 (mm) REVERT: C 211 ASN cc_start: 0.8034 (m-40) cc_final: 0.7649 (m110) REVERT: C 327 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7352 (ttpt) REVERT: E 205 TRP cc_start: 0.7888 (m100) cc_final: 0.7315 (t-100) REVERT: E 309 TYR cc_start: 0.8250 (m-80) cc_final: 0.7616 (m-80) REVERT: E 310 LEU cc_start: 0.8059 (tp) cc_final: 0.7816 (tt) REVERT: E 383 ARG cc_start: 0.7383 (ttt90) cc_final: 0.7131 (ttm-80) REVERT: E 472 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6533 (m-10) REVERT: E 549 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8121 (mm) outliers start: 73 outliers final: 58 residues processed: 259 average time/residue: 0.3654 time to fit residues: 155.1915 Evaluate side-chains 255 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 2.913 ------------------------------------------------------------------------------- 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 416 LEU Chi-restraints excluded: chain A residue 443 LEU 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 610 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 454 LEU 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 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 396 ASN Chi-restraints excluded: chain C residue 411 LEU 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 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 198 LEU Chi-restraints excluded: chain D residue 207 LEU 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 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 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 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 324 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 299 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 262 optimal weight: 5.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4470 r_free = 0.4470 target = 0.185743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.147493 restraints weight = 49165.049| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.48 r_work: 0.3529 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 28447 Z= 0.285 Angle : 0.672 11.833 38623 Z= 0.337 Chirality : 0.042 0.185 4305 Planarity : 0.005 0.066 5155 Dihedral : 4.491 45.845 4002 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.92 % Allowed : 13.91 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3585 helix: 1.41 (0.12), residues: 1848 sheet: -0.63 (0.26), residues: 413 loop : -0.68 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 403 HIS 0.010 0.001 HIS C 303 PHE 0.027 0.002 PHE A 630 TYR 0.025 0.002 TYR C 50 ARG 0.008 0.001 ARG D 688 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1550) hydrogen bonds : angle 4.80387 ( 4506) covalent geometry : bond 0.00668 (28447) covalent geometry : angle 0.67208 (38623) *********************** 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 286 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 203 time to evaluate : 2.961 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 118 LEU cc_start: 0.2989 (mt) cc_final: 0.2585 (mt) REVERT: A 193 GLU cc_start: 0.4544 (tt0) cc_final: 0.3776 (mm-30) REVERT: A 205 TRP cc_start: 0.6758 (t-100) cc_final: 0.6187 (t-100) REVERT: A 217 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 218 PHE cc_start: 0.4240 (m-80) cc_final: 0.3675 (m-80) REVERT: A 413 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: A 416 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7226 (tt) REVERT: A 426 MET cc_start: 0.7240 (mtp) cc_final: 0.6964 (mtm) REVERT: A 534 GLU cc_start: 0.5841 (mp0) cc_final: 0.5235 (mt-10) REVERT: A 558 ILE cc_start: 0.4553 (OUTLIER) cc_final: 0.3907 (tp) REVERT: A 623 ASN cc_start: 0.7323 (p0) cc_final: 0.6813 (p0) REVERT: A 688 ARG cc_start: 0.6614 (mmm-85) cc_final: 0.6244 (mmm-85) REVERT: B 57 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 201 LEU cc_start: 0.8311 (tp) cc_final: 0.7943 (mt) REVERT: B 215 GLU cc_start: 0.9074 (pt0) cc_final: 0.8833 (pt0) REVERT: B 319 ARG cc_start: 0.7773 (mmp-170) cc_final: 0.7517 (tpp80) REVERT: B 532 ASP cc_start: 0.6469 (t70) cc_final: 0.6093 (t70) REVERT: B 710 GLU cc_start: 0.6033 (tp30) cc_final: 0.5638 (tp30) REVERT: C 211 ASN cc_start: 0.8086 (m-40) cc_final: 0.7684 (m110) REVERT: C 603 ASP cc_start: 0.7570 (m-30) cc_final: 0.7127 (m-30) REVERT: D 135 PHE cc_start: 0.4660 (m-10) cc_final: 0.4331 (m-10) REVERT: E 205 TRP cc_start: 0.7922 (m100) cc_final: 0.7579 (t-100) REVERT: E 309 TYR cc_start: 0.8451 (m-80) cc_final: 0.7726 (m-80) REVERT: E 310 LEU cc_start: 0.8180 (tp) cc_final: 0.7951 (tt) REVERT: E 383 ARG cc_start: 0.7478 (ttt90) cc_final: 0.7144 (ttm-80) REVERT: E 472 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6436 (m-10) REVERT: E 549 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8160 (mm) outliers start: 83 outliers final: 64 residues processed: 268 average time/residue: 0.3634 time to fit residues: 159.4604 Evaluate side-chains 260 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 189 time to evaluate : 3.012 ------------------------------------------------------------------------------- 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 413 GLN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 LEU 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 610 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 661 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 78 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 454 LEU 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 72 VAL 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 315 LEU 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 396 ASN Chi-restraints excluded: chain C residue 411 LEU 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 565 VAL 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 81 VAL Chi-restraints excluded: chain D residue 130 GLN 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 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 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 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 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 128 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 307 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 246 optimal weight: 20.0000 chunk 276 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 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 612 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 = 0.4499 r_free = 0.4499 target = 0.188709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.149441 restraints weight = 49077.675| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.71 r_work: 0.3609 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3554 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= 0.149 Angle : 0.581 10.833 38623 Z= 0.288 Chirality : 0.040 0.254 4305 Planarity : 0.004 0.044 5155 Dihedral : 4.241 45.271 4002 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 14.86 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 3585 helix: 1.63 (0.12), residues: 1843 sheet: -0.37 (0.26), residues: 403 loop : -0.61 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 403 HIS 0.009 0.001 HIS B 527 PHE 0.014 0.002 PHE D 629 TYR 0.017 0.002 TYR C 557 ARG 0.010 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 1550) hydrogen bonds : angle 4.48115 ( 4506) covalent geometry : bond 0.00342 (28447) covalent geometry : angle 0.58121 (38623) *********************** 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 266 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.3008 (mt) cc_final: 0.2630 (mt) REVERT: A 193 GLU cc_start: 0.4491 (tt0) cc_final: 0.3815 (mm-30) REVERT: A 205 TRP cc_start: 0.6763 (t-100) cc_final: 0.6212 (t-100) REVERT: A 217 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 218 PHE cc_start: 0.4289 (m-80) cc_final: 0.3757 (m-80) REVERT: A 416 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7164 (tt) REVERT: A 426 MET cc_start: 0.7213 (mtp) cc_final: 0.6998 (mtm) REVERT: A 494 ARG cc_start: 0.7032 (mtt90) cc_final: 0.6818 (ppt170) REVERT: A 534 GLU cc_start: 0.5758 (mp0) cc_final: 0.5103 (mt-10) REVERT: A 558 ILE cc_start: 0.4486 (OUTLIER) cc_final: 0.3825 (tp) REVERT: A 623 ASN cc_start: 0.7135 (p0) cc_final: 0.6601 (p0) REVERT: B 201 LEU cc_start: 0.8311 (tp) cc_final: 0.7973 (mt) REVERT: B 215 GLU cc_start: 0.9003 (pt0) cc_final: 0.8769 (pt0) REVERT: B 319 ARG cc_start: 0.7871 (mmp-170) cc_final: 0.7550 (tpp80) REVERT: B 361 VAL cc_start: 0.8590 (t) cc_final: 0.8388 (t) REVERT: B 532 ASP cc_start: 0.6241 (t70) cc_final: 0.5890 (t70) REVERT: C 57 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8604 (mm) REVERT: C 132 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: C 211 ASN cc_start: 0.8089 (m-40) cc_final: 0.7679 (m110) REVERT: D 386 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: E 205 TRP cc_start: 0.7902 (m100) cc_final: 0.7539 (t-100) REVERT: E 309 TYR cc_start: 0.8397 (m-80) cc_final: 0.8021 (m-80) REVERT: E 310 LEU cc_start: 0.8067 (tp) cc_final: 0.7833 (tt) REVERT: E 383 ARG cc_start: 0.7431 (ttt90) cc_final: 0.7106 (ttm-80) REVERT: E 472 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6444 (m-10) REVERT: E 549 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8115 (mm) outliers start: 65 outliers final: 51 residues processed: 253 average time/residue: 0.3761 time to fit residues: 156.4726 Evaluate side-chains 249 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 3.185 ------------------------------------------------------------------------------- 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 217 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 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 661 LEU Chi-restraints excluded: chain B residue 39 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 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 72 VAL 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 315 LEU 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 396 ASN 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 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 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 517 LEU Chi-restraints excluded: chain D residue 565 VAL 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 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 630 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 277 optimal weight: 0.0030 chunk 96 optimal weight: 3.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 GLN ** 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.188723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.149626 restraints weight = 48953.513| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 4.05 r_work: 0.3586 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28447 Z= 0.153 Angle : 0.584 11.380 38623 Z= 0.287 Chirality : 0.040 0.262 4305 Planarity : 0.004 0.043 5155 Dihedral : 4.192 46.313 4002 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.18 % Allowed : 15.14 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3585 helix: 1.66 (0.12), residues: 1849 sheet: -0.44 (0.26), residues: 415 loop : -0.51 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 403 HIS 0.004 0.001 HIS C 303 PHE 0.022 0.002 PHE C 135 TYR 0.018 0.002 TYR C 557 ARG 0.009 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1550) hydrogen bonds : angle 4.45821 ( 4506) covalent geometry : bond 0.00354 (28447) covalent geometry : angle 0.58386 (38623) ********************** 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 261 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 2.852 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 118 LEU cc_start: 0.3059 (mt) cc_final: 0.2696 (mt) REVERT: A 193 GLU cc_start: 0.4379 (tt0) cc_final: 0.3686 (mm-30) REVERT: A 205 TRP cc_start: 0.6740 (t-100) cc_final: 0.6220 (t-100) REVERT: A 217 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 218 PHE cc_start: 0.4413 (m-80) cc_final: 0.3882 (m-80) REVERT: A 413 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: A 416 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7211 (tt) REVERT: A 494 ARG cc_start: 0.7095 (mtt90) cc_final: 0.6833 (ppt170) REVERT: A 534 GLU cc_start: 0.5793 (mp0) cc_final: 0.5114 (mt-10) REVERT: A 558 ILE cc_start: 0.4542 (OUTLIER) cc_final: 0.3842 (tp) REVERT: A 623 ASN cc_start: 0.7157 (p0) cc_final: 0.6617 (p0) REVERT: B 201 LEU cc_start: 0.8300 (tp) cc_final: 0.7956 (mt) REVERT: B 215 GLU cc_start: 0.9024 (pt0) cc_final: 0.8793 (pt0) REVERT: B 319 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.7548 (tpp80) REVERT: B 532 ASP cc_start: 0.6263 (t70) cc_final: 0.5905 (t70) REVERT: C 57 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8577 (mm) REVERT: C 132 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: C 211 ASN cc_start: 0.8047 (m-40) cc_final: 0.7654 (m110) REVERT: D 386 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: E 205 TRP cc_start: 0.7819 (m100) cc_final: 0.7431 (t-100) REVERT: E 309 TYR cc_start: 0.8432 (m-80) cc_final: 0.8091 (m-80) REVERT: E 310 LEU cc_start: 0.8093 (tp) cc_final: 0.7855 (tt) REVERT: E 383 ARG cc_start: 0.7484 (ttt90) cc_final: 0.7163 (ttm-80) REVERT: E 472 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6637 (m-10) REVERT: E 549 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (mm) outliers start: 62 outliers final: 50 residues processed: 247 average time/residue: 0.3740 time to fit residues: 150.2639 Evaluate side-chains 247 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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 217 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 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 661 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 322 THR 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 72 VAL 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 315 LEU 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 396 ASN Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 456 THR 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 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 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 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 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 630 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 94 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 335 optimal weight: 50.0000 chunk 289 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 268 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 GLN ** 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 396 ASN ** 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 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4507 r_free = 0.4507 target = 0.189462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.150459 restraints weight = 49115.808| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.71 r_work: 0.3597 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28447 Z= 0.136 Angle : 0.571 10.811 38623 Z= 0.281 Chirality : 0.039 0.259 4305 Planarity : 0.004 0.044 5155 Dihedral : 4.122 46.571 4002 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.29 % Allowed : 15.04 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3585 helix: 1.72 (0.12), residues: 1852 sheet: -0.35 (0.25), residues: 431 loop : -0.43 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 403 HIS 0.004 0.001 HIS C 303 PHE 0.027 0.001 PHE C 119 TYR 0.017 0.002 TYR C 557 ARG 0.008 0.000 ARG D 688 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1550) hydrogen bonds : angle 4.35989 ( 4506) covalent geometry : bond 0.00312 (28447) covalent geometry : angle 0.57065 (38623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14830.05 seconds wall clock time: 256 minutes 48.38 seconds (15408.38 seconds total)