Starting phenix.real_space_refine on Tue Jun 24 01:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k90_36970/06_2025/8k90_36970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k90_36970/06_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_36970/06_2025/8k90_36970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k90_36970/06_2025/8k90_36970.map" model { file = "/net/cci-nas-00/data/ceres_data/8k90_36970/06_2025/8k90_36970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k90_36970/06_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): 0.81s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.26, per 1000 atoms: 0.58 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: 6.68 Conformation dependent library (CDL) restraints added in 3.3 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: 3.63 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: 11.59 Time building geometry restraints manager: 7.90 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 62.350 Find NCS groups from input model: 1.530 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.020 ------------------------------------------------------------------------------- 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 : 3.141 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: 0.4529 time to fit residues: 331.1214 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 : 3.180 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.137057 restraints weight = 48707.498| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.00 r_work: 0.3605 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 3.151 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: 0.5099 (m-80) cc_final: 0.3925 (m-10) REVERT: A 64 LEU cc_start: 0.7438 (mm) cc_final: 0.6717 (tt) REVERT: A 118 LEU cc_start: 0.3313 (OUTLIER) cc_final: 0.2785 (mt) REVERT: A 128 LYS cc_start: 0.2536 (mmtm) cc_final: 0.2049 (mmtt) REVERT: A 193 GLU cc_start: 0.4889 (tt0) cc_final: 0.4223 (mm-30) REVERT: A 200 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.7255 (ptt90) REVERT: A 276 ARG cc_start: 0.6520 (mtp180) cc_final: 0.6296 (mmt90) REVERT: A 303 HIS cc_start: 0.7439 (m-70) cc_final: 0.6847 (m170) REVERT: A 426 MET cc_start: 0.7180 (mtm) cc_final: 0.6889 (mtm) REVERT: A 534 GLU cc_start: 0.5902 (mp0) cc_final: 0.4990 (mt-10) REVERT: A 574 ASN cc_start: 0.6651 (p0) cc_final: 0.5908 (t0) REVERT: B 37 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7409 (pt0) REVERT: B 87 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8089 (tptt) REVERT: B 201 LEU cc_start: 0.8439 (tp) cc_final: 0.8123 (mt) REVERT: B 215 GLU cc_start: 0.9230 (pt0) cc_final: 0.9024 (pt0) REVERT: B 217 LEU cc_start: 0.8534 (mt) cc_final: 0.8097 (mt) REVERT: B 231 LEU cc_start: 0.8994 (tp) cc_final: 0.8790 (tt) REVERT: B 232 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7970 (tmm-80) REVERT: B 280 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6360 (ttp-110) REVERT: B 334 GLN cc_start: 0.8250 (mt0) cc_final: 0.8014 (mp-120) REVERT: B 348 GLU cc_start: 0.8020 (tt0) cc_final: 0.7253 (tp30) REVERT: B 382 ILE cc_start: 0.7922 (mm) cc_final: 0.7689 (mm) REVERT: C 211 ASN cc_start: 0.8298 (m-40) cc_final: 0.7670 (m110) REVERT: C 215 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8780 (mm-30) REVERT: C 269 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 271 TYR cc_start: 0.7281 (t80) cc_final: 0.6975 (t80) REVERT: C 319 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7802 (ttp80) REVERT: C 334 GLN cc_start: 0.8302 (mt0) cc_final: 0.8042 (mt0) REVERT: C 342 GLN cc_start: 0.7361 (pt0) cc_final: 0.7084 (mp10) REVERT: C 395 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7919 (tp30) REVERT: C 405 LEU cc_start: 0.8420 (tp) cc_final: 0.8173 (mm) REVERT: C 494 ARG cc_start: 0.8847 (mtt-85) cc_final: 0.8612 (mtt-85) REVERT: C 579 GLU cc_start: 0.5329 (mp0) cc_final: 0.4955 (pm20) REVERT: C 683 ILE cc_start: 0.8436 (mt) cc_final: 0.8212 (mt) REVERT: D 219 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6796 (mt0) REVERT: D 454 LEU cc_start: 0.8369 (tt) cc_final: 0.7848 (mm) REVERT: E 6 GLU cc_start: 0.7034 (pp20) cc_final: 0.6553 (mm-30) REVERT: E 52 VAL cc_start: 0.8686 (t) cc_final: 0.8411 (t) REVERT: E 103 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: E 205 TRP cc_start: 0.8013 (m100) cc_final: 0.7262 (m-10) REVERT: E 231 LEU cc_start: 0.8192 (tp) cc_final: 0.7983 (mt) REVERT: E 241 THR cc_start: 0.7308 (m) cc_final: 0.7076 (m) REVERT: E 323 TRP cc_start: 0.7864 (t-100) cc_final: 0.7529 (t-100) REVERT: E 348 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8271 (tt0) REVERT: E 368 GLU cc_start: 0.5253 (mm-30) cc_final: 0.4891 (mt-10) REVERT: E 383 ARG cc_start: 0.7120 (ttt90) cc_final: 0.6514 (ttm-80) REVERT: E 385 GLU cc_start: 0.6481 (mt-10) cc_final: 0.5669 (tt0) REVERT: E 475 GLU cc_start: 0.4924 (mm-30) cc_final: 0.4687 (mp0) outliers start: 35 outliers final: 26 residues processed: 339 average time/residue: 0.5178 time to fit residues: 275.5658 Evaluate side-chains 272 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 3.562 ------------------------------------------------------------------------------- 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: 30.0000 chunk 72 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 55 optimal weight: 6.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.192380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.155195 restraints weight = 49111.731| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.61 r_work: 0.3622 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2071 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= 0.145 Angle : 0.555 9.158 38623 Z= 0.280 Chirality : 0.039 0.183 4305 Planarity : 0.004 0.050 5155 Dihedral : 4.047 44.837 4002 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.48 % Allowed : 9.40 % Favored : 89.12 % 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: 1.14 (0.14), residues: 3585 helix: 1.69 (0.12), residues: 1864 sheet: 0.05 (0.26), residues: 421 loop : -0.30 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 403 HIS 0.006 0.001 HIS A 208 PHE 0.015 0.001 PHE B 629 TYR 0.023 0.002 TYR B 271 ARG 0.010 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 1550) hydrogen bonds : angle 4.55136 ( 4506) covalent geometry : bond 0.00330 (28447) covalent geometry : angle 0.55483 (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 308 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 2.982 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: 0.7528 (mm) cc_final: 0.6583 (tt) REVERT: A 193 GLU cc_start: 0.4572 (tt0) cc_final: 0.3966 (mm-30) REVERT: A 205 TRP cc_start: 0.6747 (t-100) cc_final: 0.6318 (t-100) REVERT: A 303 HIS cc_start: 0.6955 (m-70) cc_final: 0.6684 (m170) REVERT: A 534 GLU cc_start: 0.5618 (mp0) cc_final: 0.4872 (mt-10) REVERT: A 574 ASN cc_start: 0.6805 (p0) cc_final: 0.6192 (t0) REVERT: A 623 ASN cc_start: 0.6705 (p0) cc_final: 0.6223 (p0) REVERT: B 57 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8244 (tt) REVERT: B 201 LEU cc_start: 0.8367 (tp) cc_final: 0.8041 (mt) REVERT: B 215 GLU cc_start: 0.8998 (pt0) cc_final: 0.8756 (pt0) REVERT: B 217 LEU cc_start: 0.8384 (mt) cc_final: 0.8030 (mt) REVERT: B 296 LEU cc_start: 0.8556 (mt) cc_final: 0.8048 (tp) REVERT: B 348 GLU cc_start: 0.7917 (tt0) cc_final: 0.7441 (tp30) REVERT: C 132 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: C 211 ASN cc_start: 0.8019 (m-40) cc_final: 0.7445 (m110) REVERT: C 215 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8529 (mm-30) REVERT: C 269 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 405 LEU cc_start: 0.8429 (tp) cc_final: 0.8201 (mm) REVERT: D 219 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6966 (mm-40) REVERT: E 6 GLU cc_start: 0.6909 (pp20) cc_final: 0.6569 (mm-30) REVERT: E 205 TRP cc_start: 0.7682 (m100) cc_final: 0.7018 (m-10) REVERT: E 383 ARG cc_start: 0.7335 (ttt90) cc_final: 0.6931 (ttm-80) REVERT: E 385 GLU cc_start: 0.6458 (mt-10) cc_final: 0.5924 (tt0) REVERT: E 472 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6202 (m-10) REVERT: E 549 LEU cc_start: 0.8402 (mm) cc_final: 0.8105 (mm) outliers start: 42 outliers final: 29 residues processed: 293 average time/residue: 0.4149 time to fit residues: 191.4019 Evaluate side-chains 244 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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 413 GLN 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: 8.9990 chunk 110 optimal weight: 1.9990 chunk 343 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.187330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.141743 restraints weight = 49183.652| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.80 r_work: 0.3599 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 28447 Z= 0.280 Angle : 0.673 9.838 38623 Z= 0.341 Chirality : 0.042 0.164 4305 Planarity : 0.005 0.064 5155 Dihedral : 4.355 44.477 4002 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.39 % Allowed : 11.09 % Favored : 86.51 % 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: 0.75 (0.14), residues: 3585 helix: 1.43 (0.12), residues: 1868 sheet: -0.30 (0.25), residues: 434 loop : -0.51 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 403 HIS 0.013 0.001 HIS C 303 PHE 0.029 0.002 PHE A 630 TYR 0.029 0.003 TYR C 50 ARG 0.009 0.001 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 1550) hydrogen bonds : angle 4.79575 ( 4506) covalent geometry : bond 0.00654 (28447) covalent geometry : angle 0.67339 (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 299 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 3.240 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 118 LEU cc_start: 0.2398 (mt) cc_final: 0.1798 (mt) REVERT: A 193 GLU cc_start: 0.4709 (tt0) cc_final: 0.3891 (mm-30) REVERT: A 205 TRP cc_start: 0.6704 (t-100) cc_final: 0.6173 (t-100) REVERT: A 217 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 218 PHE cc_start: 0.3962 (m-80) cc_final: 0.3327 (m-80) REVERT: A 416 LEU cc_start: 0.7363 (tt) cc_final: 0.7100 (tt) REVERT: A 534 GLU cc_start: 0.5693 (mp0) cc_final: 0.5110 (mt-10) REVERT: A 558 ILE cc_start: 0.4654 (OUTLIER) cc_final: 0.4011 (tp) REVERT: A 623 ASN cc_start: 0.7005 (p0) cc_final: 0.6595 (p0) REVERT: A 642 GLN cc_start: 0.5620 (mp10) cc_final: 0.5276 (mm-40) REVERT: B 57 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8614 (tt) REVERT: B 87 LYS cc_start: 0.8071 (tptt) cc_final: 0.7615 (tptt) REVERT: B 201 LEU cc_start: 0.8413 (tp) cc_final: 0.8043 (mt) REVERT: B 215 GLU cc_start: 0.9075 (pt0) cc_final: 0.8842 (pt0) REVERT: B 296 LEU cc_start: 0.8750 (mt) cc_final: 0.8369 (tp) REVERT: B 319 ARG cc_start: 0.7804 (mmp-170) cc_final: 0.7509 (tpp80) REVERT: B 348 GLU cc_start: 0.7743 (tt0) cc_final: 0.7506 (tp30) REVERT: B 710 GLU cc_start: 0.6002 (tp30) cc_final: 0.5701 (tp30) REVERT: C 57 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 211 ASN cc_start: 0.8155 (m-40) cc_final: 0.7489 (m110) REVERT: C 215 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8639 (mm-30) REVERT: C 603 ASP cc_start: 0.7693 (m-30) cc_final: 0.7271 (m-30) REVERT: D 319 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7307 (mtm180) REVERT: E 309 TYR cc_start: 0.8542 (m-80) cc_final: 0.7825 (m-80) REVERT: E 310 LEU cc_start: 0.8107 (tp) cc_final: 0.7776 (tt) REVERT: E 383 ARG cc_start: 0.7598 (ttt90) cc_final: 0.7179 (ttm-80) REVERT: E 472 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: E 549 LEU cc_start: 0.8514 (mm) cc_final: 0.8189 (mm) outliers start: 68 outliers final: 41 residues processed: 283 average time/residue: 0.4032 time to fit residues: 184.8000 Evaluate side-chains 239 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 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 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 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 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 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: 0.7980 chunk 291 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 0.0770 chunk 262 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 235 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.6942 ------------------------------------------------------------------------------- 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** ** A 650 ASN ** 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 211 ASN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 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 = 0.4514 r_free = 0.4514 target = 0.190154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.150602 restraints weight = 48981.657| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.54 r_work: 0.3596 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28447 Z= 0.157 Angle : 0.565 11.012 38623 Z= 0.282 Chirality : 0.039 0.192 4305 Planarity : 0.004 0.052 5155 Dihedral : 4.146 42.759 4002 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.39 % Allowed : 12.01 % Favored : 85.60 % 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: 1.00 (0.14), residues: 3585 helix: 1.63 (0.12), residues: 1861 sheet: -0.15 (0.26), residues: 407 loop : -0.41 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 403 HIS 0.006 0.001 HIS C 303 PHE 0.016 0.002 PHE A 630 TYR 0.019 0.002 TYR C 50 ARG 0.006 0.000 ARG B 298 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1550) hydrogen bonds : angle 4.48743 ( 4506) covalent geometry : bond 0.00360 (28447) covalent geometry : angle 0.56506 (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 281 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 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: A 193 GLU cc_start: 0.4598 (tt0) cc_final: 0.3890 (mm-30) REVERT: A 205 TRP cc_start: 0.6729 (t-100) cc_final: 0.6126 (t-100) REVERT: A 217 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 218 PHE cc_start: 0.3989 (m-80) cc_final: 0.3406 (m-80) REVERT: A 416 LEU cc_start: 0.7480 (tt) cc_final: 0.7221 (tt) REVERT: A 426 MET cc_start: 0.7183 (mtp) cc_final: 0.6913 (mtm) REVERT: A 534 GLU cc_start: 0.5742 (mp0) cc_final: 0.5094 (mt-10) REVERT: A 558 ILE cc_start: 0.4584 (OUTLIER) cc_final: 0.3980 (tp) REVERT: A 623 ASN cc_start: 0.7022 (p0) cc_final: 0.6636 (p0) REVERT: A 642 GLN cc_start: 0.5338 (mp10) cc_final: 0.5017 (mm-40) REVERT: B 57 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8343 (tt) REVERT: B 87 LYS cc_start: 0.8010 (tptt) cc_final: 0.7591 (tptt) REVERT: B 201 LEU cc_start: 0.8416 (tp) cc_final: 0.8046 (mt) REVERT: B 215 GLU cc_start: 0.9074 (pt0) cc_final: 0.8846 (pt0) REVERT: B 282 ASP cc_start: 0.7693 (m-30) cc_final: 0.7310 (t0) REVERT: B 296 LEU cc_start: 0.8727 (mt) cc_final: 0.8288 (tp) REVERT: B 348 GLU cc_start: 0.7844 (tt0) cc_final: 0.7553 (tp30) REVERT: C 211 ASN cc_start: 0.8111 (m-40) cc_final: 0.7456 (m110) REVERT: C 215 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8546 (mm-30) REVERT: C 327 LYS cc_start: 0.7611 (ttpt) cc_final: 0.7327 (ttpt) REVERT: D 386 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: E 205 TRP cc_start: 0.7868 (m100) cc_final: 0.7485 (t-100) REVERT: E 309 TYR cc_start: 0.8447 (m-80) cc_final: 0.7899 (m-80) REVERT: E 310 LEU cc_start: 0.8105 (tp) cc_final: 0.7886 (tt) REVERT: E 383 ARG cc_start: 0.7388 (ttt90) cc_final: 0.7163 (ttm-80) REVERT: E 549 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8166 (mm) outliers start: 68 outliers final: 47 residues processed: 267 average time/residue: 0.3821 time to fit residues: 167.2862 Evaluate side-chains 243 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 57 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 517 LEU 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 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 322 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 450 LEU 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: 3.9990 chunk 22 optimal weight: 20.0000 chunk 317 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 336 optimal weight: 0.0270 chunk 85 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.187396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.142019 restraints weight = 49077.888| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.77 r_work: 0.3615 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 28447 Z= 0.240 Angle : 0.622 11.018 38623 Z= 0.311 Chirality : 0.041 0.350 4305 Planarity : 0.005 0.055 5155 Dihedral : 4.243 44.115 4002 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.68 % Allowed : 13.03 % Favored : 84.30 % 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: 0.86 (0.14), residues: 3585 helix: 1.55 (0.12), residues: 1865 sheet: -0.32 (0.26), residues: 408 loop : -0.49 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 403 HIS 0.009 0.001 HIS C 303 PHE 0.022 0.002 PHE A 630 TYR 0.024 0.002 TYR C 50 ARG 0.018 0.001 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1550) hydrogen bonds : angle 4.59528 ( 4506) covalent geometry : bond 0.00560 (28447) covalent geometry : angle 0.62233 (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 285 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 209 time to evaluate : 2.860 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: 0.7483 (mm) cc_final: 0.6547 (tt) REVERT: A 193 GLU cc_start: 0.4720 (tt0) cc_final: 0.3911 (mm-30) REVERT: A 205 TRP cc_start: 0.6697 (t-100) cc_final: 0.6084 (t-100) REVERT: A 217 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 218 PHE cc_start: 0.4071 (m-80) cc_final: 0.3462 (m-80) REVERT: A 416 LEU cc_start: 0.7462 (tt) cc_final: 0.7182 (tt) REVERT: A 426 MET cc_start: 0.7296 (mtp) cc_final: 0.7014 (mtm) REVERT: A 534 GLU cc_start: 0.5774 (mp0) cc_final: 0.5212 (mt-10) REVERT: A 558 ILE cc_start: 0.4530 (OUTLIER) cc_final: 0.3899 (tp) REVERT: A 623 ASN cc_start: 0.7195 (p0) cc_final: 0.6813 (p0) REVERT: A 642 GLN cc_start: 0.5440 (mp10) cc_final: 0.5146 (mm-40) REVERT: B 57 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 87 LYS cc_start: 0.8095 (tptt) cc_final: 0.7709 (tptt) REVERT: B 201 LEU cc_start: 0.8398 (tp) cc_final: 0.8015 (mt) REVERT: B 215 GLU cc_start: 0.9019 (pt0) cc_final: 0.8769 (pt0) REVERT: B 319 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7474 (tpp80) REVERT: B 348 GLU cc_start: 0.7809 (tt0) cc_final: 0.7580 (tp30) REVERT: B 527 HIS cc_start: 0.6440 (t-90) cc_final: 0.6142 (t70) REVERT: B 710 GLU cc_start: 0.5885 (tp30) cc_final: 0.5549 (tp30) REVERT: C 57 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8706 (mm) REVERT: C 211 ASN cc_start: 0.8213 (m-40) cc_final: 0.7527 (m110) REVERT: C 215 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8668 (mm-30) REVERT: C 327 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7437 (ttpt) REVERT: C 603 ASP cc_start: 0.7589 (m-30) cc_final: 0.7173 (m-30) REVERT: D 135 PHE cc_start: 0.4512 (m-10) cc_final: 0.3794 (m-10) REVERT: D 681 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7578 (mt) REVERT: E 52 VAL cc_start: 0.8538 (t) cc_final: 0.8287 (t) REVERT: E 309 TYR cc_start: 0.8582 (m-80) cc_final: 0.7984 (m-80) REVERT: E 310 LEU cc_start: 0.8102 (tp) cc_final: 0.7841 (tt) REVERT: E 383 ARG cc_start: 0.7557 (ttt90) cc_final: 0.7287 (ttm-80) REVERT: E 472 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6555 (m-10) REVERT: E 549 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (mm) outliers start: 76 outliers final: 58 residues processed: 270 average time/residue: 0.3867 time to fit residues: 171.2004 Evaluate side-chains 260 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 2.945 ------------------------------------------------------------------------------- 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 356 MET 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 674 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 322 THR 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 517 LEU Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 681 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 215 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 164 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 318 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.189674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.150813 restraints weight = 48933.910| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.59 r_work: 0.3600 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28447 Z= 0.161 Angle : 0.570 10.605 38623 Z= 0.282 Chirality : 0.039 0.200 4305 Planarity : 0.004 0.045 5155 Dihedral : 4.140 43.782 4002 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.75 % Allowed : 13.20 % Favored : 84.05 % 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: 0.98 (0.14), residues: 3585 helix: 1.67 (0.12), residues: 1864 sheet: -0.28 (0.26), residues: 411 loop : -0.46 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 403 HIS 0.005 0.001 HIS C 303 PHE 0.016 0.002 PHE A 630 TYR 0.019 0.002 TYR B 227 ARG 0.008 0.000 ARG E 665 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 1550) hydrogen bonds : angle 4.43229 ( 4506) covalent geometry : bond 0.00369 (28447) covalent geometry : angle 0.56962 (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 289 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 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: symmetry clash REVERT: A 64 LEU cc_start: 0.7518 (mm) cc_final: 0.6547 (tt) REVERT: A 118 LEU cc_start: 0.2639 (mt) cc_final: 0.2300 (mt) REVERT: A 193 GLU cc_start: 0.4315 (tt0) cc_final: 0.3706 (mm-30) REVERT: A 205 TRP cc_start: 0.6698 (t-100) cc_final: 0.6201 (t-100) REVERT: A 217 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7662 (mm) REVERT: A 218 PHE cc_start: 0.3833 (m-80) cc_final: 0.3343 (m-80) REVERT: A 416 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7148 (tt) REVERT: A 426 MET cc_start: 0.7298 (mtp) cc_final: 0.7050 (mtm) REVERT: A 534 GLU cc_start: 0.5570 (mp0) cc_final: 0.4961 (mt-10) REVERT: A 558 ILE cc_start: 0.4572 (OUTLIER) cc_final: 0.3908 (tp) REVERT: A 623 ASN cc_start: 0.7078 (p0) cc_final: 0.6743 (p0) REVERT: A 642 GLN cc_start: 0.5303 (mp10) cc_final: 0.5065 (mm-40) REVERT: B 57 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8273 (tt) REVERT: B 87 LYS cc_start: 0.8099 (tptt) cc_final: 0.7704 (tptt) REVERT: B 201 LEU cc_start: 0.8308 (tp) cc_final: 0.7973 (mt) REVERT: B 215 GLU cc_start: 0.8838 (pt0) cc_final: 0.8615 (pt0) REVERT: B 282 ASP cc_start: 0.7431 (t0) cc_final: 0.6909 (t0) REVERT: B 296 LEU cc_start: 0.8875 (tp) cc_final: 0.8512 (tp) REVERT: C 57 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 211 ASN cc_start: 0.8007 (m-40) cc_final: 0.7440 (m110) REVERT: C 327 LYS cc_start: 0.7604 (ttpt) cc_final: 0.7355 (ttpt) REVERT: D 386 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8602 (m-80) REVERT: E 205 TRP cc_start: 0.7633 (m100) cc_final: 0.7153 (t-100) REVERT: E 309 TYR cc_start: 0.8470 (m-80) cc_final: 0.7994 (m-80) REVERT: E 383 ARG cc_start: 0.7416 (ttt90) cc_final: 0.7168 (ttm-80) REVERT: E 472 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6421 (m-10) REVERT: E 549 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8088 (mm) outliers start: 78 outliers final: 56 residues processed: 271 average time/residue: 0.3495 time to fit residues: 157.3981 Evaluate side-chains 259 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 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 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 674 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 LEU 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 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 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 322 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 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 600 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: 10.0000 chunk 304 optimal weight: 30.0000 chunk 299 optimal weight: 0.9990 chunk 337 optimal weight: 30.0000 chunk 105 optimal weight: 0.2980 chunk 213 optimal weight: 6.9990 chunk 351 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.187705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142426 restraints weight = 48898.654| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.81 r_work: 0.3606 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28447 Z= 0.205 Angle : 0.610 11.670 38623 Z= 0.302 Chirality : 0.040 0.253 4305 Planarity : 0.004 0.051 5155 Dihedral : 4.218 44.157 4002 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.78 % Allowed : 13.73 % Favored : 83.49 % 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: 0.92 (0.14), residues: 3585 helix: 1.64 (0.12), residues: 1858 sheet: -0.33 (0.26), residues: 405 loop : -0.49 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 403 HIS 0.007 0.001 HIS C 303 PHE 0.020 0.002 PHE A 630 TYR 0.020 0.002 TYR C 50 ARG 0.007 0.000 ARG D 688 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1550) hydrogen bonds : angle 4.54472 ( 4506) covalent geometry : bond 0.00479 (28447) covalent geometry : angle 0.61016 (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 278 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7510 (mm) cc_final: 0.6580 (tt) REVERT: A 118 LEU cc_start: 0.2942 (mt) cc_final: 0.2528 (mt) REVERT: A 193 GLU cc_start: 0.4619 (tt0) cc_final: 0.3853 (mm-30) REVERT: A 205 TRP cc_start: 0.6725 (t-100) cc_final: 0.6187 (t-100) REVERT: A 217 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 218 PHE cc_start: 0.4108 (m-80) cc_final: 0.3582 (m-80) REVERT: A 416 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7184 (tt) REVERT: A 534 GLU cc_start: 0.5733 (mp0) cc_final: 0.5108 (mt-10) REVERT: A 558 ILE cc_start: 0.4526 (OUTLIER) cc_final: 0.3894 (tp) REVERT: A 623 ASN cc_start: 0.7213 (p0) cc_final: 0.6842 (p0) REVERT: A 642 GLN cc_start: 0.5386 (mp10) cc_final: 0.5059 (mm-40) REVERT: B 57 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 87 LYS cc_start: 0.8326 (tptt) cc_final: 0.8027 (mttm) REVERT: B 201 LEU cc_start: 0.8383 (tp) cc_final: 0.8003 (mt) REVERT: B 203 ARG cc_start: 0.7577 (tpt170) cc_final: 0.7012 (tpt170) REVERT: B 215 GLU cc_start: 0.9054 (pt0) cc_final: 0.8820 (pt0) REVERT: B 296 LEU cc_start: 0.8915 (tp) cc_final: 0.8681 (tp) REVERT: B 319 ARG cc_start: 0.7737 (mmp-170) cc_final: 0.7377 (tpp80) REVERT: C 57 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 211 ASN cc_start: 0.8090 (m-40) cc_final: 0.7697 (m110) REVERT: C 327 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7329 (ttpt) REVERT: C 603 ASP cc_start: 0.7402 (m-30) cc_final: 0.6971 (m-30) REVERT: D 135 PHE cc_start: 0.4663 (m-10) cc_final: 0.4076 (m-10) REVERT: D 194 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7819 (tp) REVERT: D 368 GLU cc_start: 0.6734 (tp30) cc_final: 0.6319 (tp30) REVERT: E 52 VAL cc_start: 0.8393 (t) cc_final: 0.8150 (t) REVERT: E 205 TRP cc_start: 0.7908 (m100) cc_final: 0.7539 (t-100) REVERT: E 309 TYR cc_start: 0.8383 (m-80) cc_final: 0.8006 (m-80) REVERT: E 383 ARG cc_start: 0.7339 (ttt90) cc_final: 0.7075 (ttm-80) REVERT: E 472 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: E 549 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8172 (mm) outliers start: 79 outliers final: 62 residues processed: 260 average time/residue: 0.3963 time to fit residues: 171.5479 Evaluate side-chains 262 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 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 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 674 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 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 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 254 LEU 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 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 194 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 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 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 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: 4.9990 chunk 161 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 307 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 246 optimal weight: 20.0000 chunk 276 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.6782 ------------------------------------------------------------------------------- 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 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 = 0.4501 r_free = 0.4501 target = 0.188908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.150237 restraints weight = 48999.797| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.85 r_work: 0.3605 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28447 Z= 0.151 Angle : 0.571 11.004 38623 Z= 0.281 Chirality : 0.039 0.273 4305 Planarity : 0.004 0.043 5155 Dihedral : 4.123 44.000 4002 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.54 % Allowed : 14.05 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.14), residues: 3585 helix: 1.77 (0.12), residues: 1853 sheet: -0.30 (0.25), residues: 434 loop : -0.46 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 403 HIS 0.006 0.001 HIS B 527 PHE 0.014 0.001 PHE D 629 TYR 0.017 0.002 TYR C 557 ARG 0.007 0.000 ARG D 688 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1550) hydrogen bonds : angle 4.39167 ( 4506) covalent geometry : bond 0.00348 (28447) covalent geometry : angle 0.57104 (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 271 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7468 (mm) cc_final: 0.6514 (tt) REVERT: A 118 LEU cc_start: 0.2940 (mt) cc_final: 0.2575 (mt) REVERT: A 193 GLU cc_start: 0.4513 (tt0) cc_final: 0.3851 (mm-30) REVERT: A 205 TRP cc_start: 0.6767 (t-100) cc_final: 0.6226 (t-100) REVERT: A 217 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 218 PHE cc_start: 0.3985 (m-80) cc_final: 0.3516 (m-80) REVERT: A 416 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7185 (tt) REVERT: A 494 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6861 (ppt170) REVERT: A 534 GLU cc_start: 0.5665 (mp0) cc_final: 0.5034 (mt-10) REVERT: A 558 ILE cc_start: 0.4552 (OUTLIER) cc_final: 0.3875 (tp) REVERT: A 623 ASN cc_start: 0.7091 (p0) cc_final: 0.6549 (p0) REVERT: A 642 GLN cc_start: 0.5343 (mp10) cc_final: 0.5053 (mm-40) REVERT: B 201 LEU cc_start: 0.8344 (tp) cc_final: 0.7984 (mt) REVERT: B 215 GLU cc_start: 0.8943 (pt0) cc_final: 0.8699 (pt0) REVERT: B 532 ASP cc_start: 0.6220 (t70) cc_final: 0.5708 (t70) REVERT: C 57 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (mm) REVERT: C 132 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7369 (pp20) REVERT: C 211 ASN cc_start: 0.8016 (m-40) cc_final: 0.7643 (m110) REVERT: C 327 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7396 (ttpt) REVERT: D 135 PHE cc_start: 0.4700 (m-10) cc_final: 0.4089 (m-10) REVERT: D 194 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7808 (tp) REVERT: D 386 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: E 205 TRP cc_start: 0.7790 (m100) cc_final: 0.7400 (t-100) REVERT: E 309 TYR cc_start: 0.8323 (m-80) cc_final: 0.8006 (m-80) REVERT: E 383 ARG cc_start: 0.7420 (ttt90) cc_final: 0.7136 (ttm-80) REVERT: E 472 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: E 549 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (mm) outliers start: 72 outliers final: 52 residues processed: 253 average time/residue: 0.4919 time to fit residues: 213.9941 Evaluate side-chains 252 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 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 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 VAL 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 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 194 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 630 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 118 optimal weight: 0.4980 chunk 91 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 25 optimal weight: 0.0060 chunk 46 optimal weight: 5.9990 chunk 277 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 612 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4526 r_free = 0.4526 target = 0.191183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.152784 restraints weight = 48901.095| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.61 r_work: 0.3614 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28447 Z= 0.116 Angle : 0.561 12.055 38623 Z= 0.274 Chirality : 0.039 0.274 4305 Planarity : 0.004 0.042 5155 Dihedral : 4.025 44.344 4002 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.08 % Allowed : 14.37 % Favored : 83.56 % 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: 1.85 (0.12), residues: 1858 sheet: -0.15 (0.25), residues: 440 loop : -0.41 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 403 HIS 0.003 0.001 HIS A 303 PHE 0.020 0.001 PHE C 135 TYR 0.017 0.002 TYR C 238 ARG 0.008 0.000 ARG D 688 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 1550) hydrogen bonds : angle 4.26337 ( 4506) covalent geometry : bond 0.00261 (28447) covalent geometry : angle 0.56100 (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 271 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 2.949 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 64 LEU cc_start: 0.7494 (mm) cc_final: 0.6650 (tt) REVERT: A 118 LEU cc_start: 0.2925 (mt) cc_final: 0.2518 (mt) REVERT: A 193 GLU cc_start: 0.4571 (tt0) cc_final: 0.3814 (mm-30) REVERT: A 205 TRP cc_start: 0.6704 (t-100) cc_final: 0.6166 (t-100) REVERT: A 217 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7816 (mm) REVERT: A 218 PHE cc_start: 0.4127 (m-80) cc_final: 0.3669 (m-80) REVERT: A 416 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7243 (tt) REVERT: A 494 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6788 (ppt170) REVERT: A 534 GLU cc_start: 0.5722 (mp0) cc_final: 0.5107 (mt-10) REVERT: A 558 ILE cc_start: 0.4571 (OUTLIER) cc_final: 0.3942 (tp) REVERT: A 623 ASN cc_start: 0.7092 (p0) cc_final: 0.6505 (p0) REVERT: B 87 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8345 (ptpt) REVERT: B 201 LEU cc_start: 0.8354 (tp) cc_final: 0.7999 (mt) REVERT: B 215 GLU cc_start: 0.9069 (pt0) cc_final: 0.8848 (pt0) REVERT: B 532 ASP cc_start: 0.6174 (t70) cc_final: 0.5650 (t70) REVERT: B 650 ASN cc_start: 0.8300 (m-40) cc_final: 0.8055 (t0) REVERT: C 57 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8536 (mm) REVERT: C 132 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7407 (pp20) REVERT: C 211 ASN cc_start: 0.8078 (m-40) cc_final: 0.7655 (m110) REVERT: D 135 PHE cc_start: 0.4718 (m-10) cc_final: 0.4092 (m-10) REVERT: D 219 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6606 (mt0) REVERT: E 205 TRP cc_start: 0.7968 (m100) cc_final: 0.7598 (t-100) REVERT: E 383 ARG cc_start: 0.7355 (ttt90) cc_final: 0.7093 (ttm-80) REVERT: E 472 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: E 549 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8213 (mm) outliers start: 59 outliers final: 45 residues processed: 257 average time/residue: 0.3828 time to fit residues: 165.0334 Evaluate side-chains 252 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 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 499 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 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 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 417 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 115 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 630 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 94 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 327 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 268 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 543 HIS ** 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 = 0.4510 r_free = 0.4510 target = 0.189861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.150662 restraints weight = 49077.340| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.71 r_work: 0.3607 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28447 Z= 0.138 Angle : 0.571 11.492 38623 Z= 0.278 Chirality : 0.039 0.275 4305 Planarity : 0.004 0.043 5155 Dihedral : 4.022 44.851 4002 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.01 % Allowed : 14.96 % Favored : 83.03 % 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: 1.20 (0.14), residues: 3585 helix: 1.85 (0.12), residues: 1859 sheet: -0.14 (0.25), residues: 440 loop : -0.36 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 403 HIS 0.004 0.001 HIS C 303 PHE 0.029 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 0.03526 ( 1550) hydrogen bonds : angle 4.27831 ( 4506) covalent geometry : bond 0.00319 (28447) covalent geometry : angle 0.57065 (38623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17137.05 seconds wall clock time: 300 minutes 53.38 seconds (18053.38 seconds total)