Starting phenix.real_space_refine on Fri May 16 10:31:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7p_44319/05_2025/9b7p_44319.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7p_44319/05_2025/9b7p_44319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7p_44319/05_2025/9b7p_44319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7p_44319/05_2025/9b7p_44319.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7p_44319/05_2025/9b7p_44319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7p_44319/05_2025/9b7p_44319.cif" } resolution = 2.98 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 9351 2.51 5 N 2548 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14771 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2332 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 271} Chain breaks: 5 Chain: "B" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain breaks: 1 Chain: "C" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3455 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 399} Chain breaks: 3 Chain: "D" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 273} Chain breaks: 5 Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 666 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain breaks: 2 Chain: "F" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3455 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 399} Chain breaks: 3 Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 787 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 975 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 8.38, per 1000 atoms: 0.57 Number of scatterers: 14771 At special positions: 0 Unit cell: (130.781, 108.29, 94.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2820 8.00 N 2548 7.00 C 9351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 111 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 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: 3.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 49 sheets defined 5.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.601A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.879A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.077A pdb=" N LEU C 435 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.879A pdb=" N ILE C 566 " --> pdb=" O GLU C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.520A pdb=" N PHE D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 563 through 567 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.320A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.976A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.954A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 563 through 569 removed outlier: 4.484A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 106 removed outlier: 3.610A pdb=" N PHE L 106 " --> pdb=" O PRO L 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 250 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 removed outlier: 4.659A pdb=" N PHE A 275 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR A 377 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261 removed outlier: 4.094A pdb=" N GLN A 646 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.054A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA7, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.216A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 629 removed outlier: 4.056A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 449 removed outlier: 5.647A pdb=" N LEU B 447 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER B 464 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.191A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 627 " --> pdb=" O TRP B 607 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB3, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.032A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 231 through 235 removed outlier: 6.333A pdb=" N THR C 676 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 319 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN C 678 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 317 " --> pdb=" O GLN C 678 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 680 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE C 315 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU C 682 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 313 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C 684 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 307 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 372 through 373 removed outlier: 9.610A pdb=" N PHE C 372 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C 246 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 676 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 319 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN C 678 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 317 " --> pdb=" O GLN C 678 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 680 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE C 315 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU C 682 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 313 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C 684 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 307 " --> pdb=" O GLN C 688 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 308 " --> pdb=" O HIS C 423 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 258 through 261 removed outlier: 7.449A pdb=" N THR C 279 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR C 379 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TRP C 281 " --> pdb=" O TYR C 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AB8, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.363A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.756A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AC2, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AC3, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC4, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.060A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 245 through 249 Processing sheet with id=AC6, first strand: chain 'D' and resid 258 through 261 removed outlier: 4.575A pdb=" N PHE D 275 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR D 377 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 258 through 261 removed outlier: 4.600A pdb=" N ILE D 647 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.216A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 483 through 484 removed outlier: 3.609A pdb=" N SER D 483 " --> pdb=" O GLN D 599 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 508 through 511 Processing sheet with id=AD2, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD3, first strand: chain 'D' and resid 619 through 621 removed outlier: 5.809A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 627 through 628 removed outlier: 6.418A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 445 through 451 removed outlier: 5.598A pdb=" N LEU E 447 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER E 464 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E 451 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N THR E 460 " --> pdb=" O ILE E 451 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.231A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET E 605 " --> pdb=" O PHE F 629 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 578 through 579 removed outlier: 3.931A pdb=" N SER F 508 " --> pdb=" O GLN E 579 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.560A pdb=" N ASP F 231 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY F 677 " --> pdb=" O TRP F 247 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR F 676 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE F 320 " --> pdb=" O THR F 676 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 312 " --> pdb=" O GLU F 684 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU F 686 " --> pdb=" O PRO F 310 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN F 688 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE F 308 " --> pdb=" O GLN F 688 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 371 through 373 removed outlier: 9.080A pdb=" N PHE F 372 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR F 246 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY F 677 " --> pdb=" O TRP F 247 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR F 676 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE F 320 " --> pdb=" O THR F 676 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 312 " --> pdb=" O GLU F 684 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU F 686 " --> pdb=" O PRO F 310 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN F 688 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE F 308 " --> pdb=" O GLN F 688 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE F 308 " --> pdb=" O HIS F 423 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 258 through 261 removed outlier: 4.221A pdb=" N PHE F 275 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR F 377 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE3, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.456A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 445 through 451 removed outlier: 6.683A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AE6, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AE7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AE8, first strand: chain 'F' and resid 578 through 581 removed outlier: 4.008A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 619 through 621 removed outlier: 5.797A pdb=" N ALA F 620 " --> pdb=" O MET F 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'L' and resid 26 through 28 Processing sheet with id=AF2, first strand: chain 'L' and resid 68 through 69 removed outlier: 3.648A pdb=" N ARG L 68 " --> pdb=" O GLN L 60 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN L 61 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL L 108 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AF4, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.772A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET H 53 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA H 52 " --> pdb=" O ASP H 118 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 768 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: 4.58 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 6971 1.43 - 1.65: 8132 1.65 - 1.87: 96 1.87 - 2.09: 0 2.09 - 2.31: 5 Bond restraints: 15204 Sorted by residual: bond pdb=" CB LEU L 35 " pdb=" CG LEU L 35 " ideal model delta sigma weight residual 1.530 2.182 -0.652 2.00e-02 2.50e+03 1.06e+03 bond pdb=" CD1 PHE L 106 " pdb=" CE1 PHE L 106 " ideal model delta sigma weight residual 1.382 2.311 -0.929 3.00e-02 1.11e+03 9.59e+02 bond pdb=" CD2 PHE L 106 " pdb=" CE2 PHE L 106 " ideal model delta sigma weight residual 1.382 2.305 -0.923 3.00e-02 1.11e+03 9.46e+02 bond pdb=" CE1 PHE L 106 " pdb=" CZ PHE L 106 " ideal model delta sigma weight residual 1.382 2.235 -0.853 3.00e-02 1.11e+03 8.08e+02 bond pdb=" CE2 PHE L 106 " pdb=" CZ PHE L 106 " ideal model delta sigma weight residual 1.382 2.230 -0.848 3.00e-02 1.11e+03 7.98e+02 ... (remaining 15199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.92: 20680 8.92 - 17.85: 7 17.85 - 26.77: 2 26.77 - 35.70: 0 35.70 - 44.62: 1 Bond angle restraints: 20690 Sorted by residual: angle pdb=" CA LEU L 35 " pdb=" CB LEU L 35 " pdb=" CG LEU L 35 " ideal model delta sigma weight residual 116.30 160.92 -44.62 3.50e+00 8.16e-02 1.63e+02 angle pdb=" CD1 LEU L 35 " pdb=" CG LEU L 35 " pdb=" CD2 LEU L 35 " ideal model delta sigma weight residual 110.80 92.97 17.83 2.20e+00 2.07e-01 6.57e+01 angle pdb=" C ILE L 81 " pdb=" N PRO L 82 " pdb=" CA PRO L 82 " ideal model delta sigma weight residual 119.89 127.71 -7.82 1.02e+00 9.61e-01 5.87e+01 angle pdb=" CB LEU L 35 " pdb=" CG LEU L 35 " pdb=" CD1 LEU L 35 " ideal model delta sigma weight residual 110.70 132.44 -21.74 3.00e+00 1.11e-01 5.25e+01 angle pdb=" N ARG C 533 " pdb=" CA ARG C 533 " pdb=" C ARG C 533 " ideal model delta sigma weight residual 111.28 119.03 -7.75 1.09e+00 8.42e-01 5.06e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 8471 17.28 - 34.55: 285 34.55 - 51.82: 60 51.82 - 69.10: 12 69.10 - 86.37: 17 Dihedral angle restraints: 8845 sinusoidal: 3505 harmonic: 5340 Sorted by residual: dihedral pdb=" CA ASP A 384 " pdb=" C ASP A 384 " pdb=" N GLY A 385 " pdb=" CA GLY A 385 " ideal model delta harmonic sigma weight residual -180.00 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA TYR C 484 " pdb=" C TYR C 484 " pdb=" N ARG C 485 " pdb=" CA ARG C 485 " ideal model delta harmonic sigma weight residual -180.00 -155.40 -24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR L 32 " pdb=" C THR L 32 " pdb=" N LEU L 33 " pdb=" CA LEU L 33 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 8842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2031 0.133 - 0.266: 76 0.266 - 0.399: 4 0.399 - 0.532: 1 0.532 - 0.664: 1 Chirality restraints: 2113 Sorted by residual: chirality pdb=" CG LEU L 35 " pdb=" CB LEU L 35 " pdb=" CD1 LEU L 35 " pdb=" CD2 LEU L 35 " both_signs ideal model delta sigma weight residual False -2.59 -1.93 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA GLN L 49 " pdb=" N GLN L 49 " pdb=" C GLN L 49 " pdb=" CB GLN L 49 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA PHE H 48 " pdb=" N PHE H 48 " pdb=" C PHE H 48 " pdb=" CB PHE H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 2110 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 106 " 0.025 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE L 106 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE L 106 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE L 106 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE L 106 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE L 106 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE L 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 126 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C GLY H 126 " 0.036 2.00e-02 2.50e+03 pdb=" O GLY H 126 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR H 127 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 87 " -0.006 2.00e-02 2.50e+03 1.49e-02 3.88e+00 pdb=" CG PHE H 87 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE H 87 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE H 87 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE H 87 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 87 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE H 87 " -0.002 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 35 2.33 - 2.98: 7493 2.98 - 3.62: 20855 3.62 - 4.26: 36392 4.26 - 4.90: 59830 Nonbonded interactions: 124605 Sorted by model distance: nonbonded pdb=" O TYR A 399 " pdb=" O CYS F 230 " model vdw 1.693 3.040 nonbonded pdb=" OH TYR D 415 " pdb=" O HIS D 642 " model vdw 2.054 3.040 nonbonded pdb=" OH TYR F 415 " pdb=" O HIS F 642 " model vdw 2.118 3.040 nonbonded pdb=" NH2 ARG A 485 " pdb=" OG SER A 576 " model vdw 2.122 3.120 nonbonded pdb=" CB TYR L 55 " pdb=" OH TYR L 114 " model vdw 2.142 3.440 ... (remaining 124600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 244 through 424 or resid 478 through 681)) } ncs_group { reference = (chain 'B' and (resid 433 through 579 or resid 592 through 610)) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.900 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.017 0.929 15206 Z= 0.663 Angle : 0.986 44.620 20694 Z= 0.571 Chirality : 0.062 0.664 2113 Planarity : 0.005 0.047 2736 Dihedral : 10.703 86.372 5445 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.69 % Allowed : 1.75 % Favored : 96.56 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.12 % 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: -1.63 (0.16), residues: 1811 helix: -4.05 (0.30), residues: 76 sheet: -0.96 (0.22), residues: 409 loop : -0.96 (0.14), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 137 HIS 0.014 0.002 HIS F 290 PHE 0.031 0.003 PHE L 106 TYR 0.029 0.003 TYR F 443 ARG 0.008 0.001 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.24756 ( 277) hydrogen bonds : angle 9.79154 ( 768) SS BOND : bond 0.00440 ( 2) SS BOND : angle 0.84736 ( 4) covalent geometry : bond 0.01715 (15204) covalent geometry : angle 0.98574 (20690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 313 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.7585 (pt0) cc_final: 0.6949 (tp40) REVERT: A 557 LYS cc_start: 0.6875 (mptt) cc_final: 0.6594 (tptp) REVERT: A 641 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8092 (OUTLIER) REVERT: C 312 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7252 (ptt90) REVERT: C 564 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: C 725 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8100 (ptp-110) REVERT: D 358 SER cc_start: 0.6476 (m) cc_final: 0.6087 (t) REVERT: D 611 ASP cc_start: 0.7104 (t0) cc_final: 0.6717 (t0) REVERT: D 641 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8307 (mttp) REVERT: E 610 ARG cc_start: 0.7156 (ttm-80) cc_final: 0.4947 (mpt180) REVERT: F 281 TRP cc_start: 0.7071 (m100) cc_final: 0.6190 (m-90) REVERT: F 460 THR cc_start: 0.7957 (t) cc_final: 0.7735 (m) REVERT: L 102 GLU cc_start: 0.6658 (mt-10) cc_final: 0.5948 (tm-30) outliers start: 27 outliers final: 14 residues processed: 338 average time/residue: 1.0040 time to fit residues: 379.9987 Evaluate side-chains 210 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 556 ASP Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 94 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 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 376 GLN A 403 GLN A 497 ASN A 498 ASN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS A 646 GLN B 452 ASN B 458 GLN C 233 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 546 GLN C 552 ASN C 585 GLN C 646 GLN C 710 ASN D 259 GLN D 579 GLN D 646 GLN D 651 ASN E 456 GLN E 474 GLN ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 419 ASN F 430 GLN F 579 GLN F 585 GLN F 592 GLN F 608 GLN F 646 GLN F 700 GLN F 710 ASN L 60 GLN H 50 ASN H 86 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132819 restraints weight = 20019.646| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.65 r_work: 0.3386 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.927 15206 Z= 0.623 Angle : 0.758 45.238 20694 Z= 0.367 Chirality : 0.048 0.681 2113 Planarity : 0.005 0.041 2736 Dihedral : 6.717 80.304 2046 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.29 % Rotamer: Outliers : 2.94 % Allowed : 8.06 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.22 (0.17), residues: 1811 helix: -3.41 (0.47), residues: 64 sheet: -0.77 (0.23), residues: 361 loop : -0.71 (0.14), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 137 HIS 0.012 0.002 HIS F 290 PHE 0.026 0.002 PHE L 106 TYR 0.022 0.002 TYR F 443 ARG 0.007 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 277) hydrogen bonds : angle 6.81625 ( 768) SS BOND : bond 0.00742 ( 2) SS BOND : angle 0.52202 ( 4) covalent geometry : bond 0.01672 (15204) covalent geometry : angle 0.75756 (20690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.726 Fit side-chains REVERT: A 254 ASN cc_start: 0.7731 (m-40) cc_final: 0.7203 (t0) REVERT: A 412 GLN cc_start: 0.7859 (pt0) cc_final: 0.6968 (tp40) REVERT: A 519 ASN cc_start: 0.7330 (t0) cc_final: 0.7052 (t0) REVERT: A 557 LYS cc_start: 0.7066 (mptt) cc_final: 0.6590 (tptp) REVERT: A 641 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8166 (mttm) REVERT: C 312 ARG cc_start: 0.7476 (mtt90) cc_final: 0.7220 (ptt90) REVERT: C 564 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: C 678 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6095 (mt0) REVERT: C 725 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8079 (ptp-110) REVERT: D 358 SER cc_start: 0.6849 (m) cc_final: 0.6373 (t) REVERT: D 641 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8283 (mttp) REVERT: E 610 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.4787 (mpt180) REVERT: F 229 HIS cc_start: 0.7353 (m90) cc_final: 0.7137 (m-70) REVERT: F 281 TRP cc_start: 0.7100 (m100) cc_final: 0.6150 (m-90) REVERT: L 55 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.4411 (p90) REVERT: L 94 PHE cc_start: 0.7055 (m-80) cc_final: 0.6831 (m-80) REVERT: L 102 GLU cc_start: 0.6642 (mt-10) cc_final: 0.5845 (tm-30) REVERT: H 22 GLN cc_start: 0.6625 (tp40) cc_final: 0.6396 (tp-100) outliers start: 47 outliers final: 17 residues processed: 238 average time/residue: 1.1061 time to fit residues: 294.0530 Evaluate side-chains 197 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 678 GLN Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 91 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 53 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 498 ASN A 646 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN E 456 GLN E 474 GLN F 229 HIS F 314 ASN F 452 ASN F 570 ASN F 585 GLN F 592 GLN L 60 GLN L 61 GLN H 58 GLN H 86 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131822 restraints weight = 19981.717| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.74 r_work: 0.3406 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.926 15206 Z= 0.617 Angle : 0.714 45.572 20694 Z= 0.337 Chirality : 0.046 0.675 2113 Planarity : 0.005 0.043 2736 Dihedral : 6.336 76.538 2038 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.75 % Allowed : 9.81 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.03 (0.17), residues: 1811 helix: -3.09 (0.53), residues: 64 sheet: -0.57 (0.24), residues: 358 loop : -0.60 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 137 HIS 0.011 0.001 HIS F 290 PHE 0.025 0.002 PHE C 629 TYR 0.018 0.002 TYR F 443 ARG 0.004 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 277) hydrogen bonds : angle 6.26135 ( 768) SS BOND : bond 0.00826 ( 2) SS BOND : angle 0.69235 ( 4) covalent geometry : bond 0.01659 (15204) covalent geometry : angle 0.71373 (20690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.458 Fit side-chains REVERT: A 254 ASN cc_start: 0.7706 (m-40) cc_final: 0.7178 (t0) REVERT: A 412 GLN cc_start: 0.7877 (pt0) cc_final: 0.6876 (tp40) REVERT: A 519 ASN cc_start: 0.7326 (t0) cc_final: 0.7071 (t0) REVERT: A 557 LYS cc_start: 0.6989 (mptt) cc_final: 0.6480 (tptp) REVERT: C 564 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: C 678 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6133 (mp10) REVERT: C 725 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8052 (ptp-110) REVERT: D 358 SER cc_start: 0.6840 (m) cc_final: 0.6270 (t) REVERT: D 641 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8390 (mttp) REVERT: E 610 ARG cc_start: 0.7018 (ttm-80) cc_final: 0.4648 (mpt180) REVERT: F 229 HIS cc_start: 0.7297 (m-70) cc_final: 0.7093 (m90) REVERT: F 233 GLN cc_start: 0.8087 (mt0) cc_final: 0.7552 (tt0) REVERT: F 425 SER cc_start: 0.8867 (p) cc_final: 0.8408 (t) REVERT: L 55 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.4126 (p90) REVERT: L 102 GLU cc_start: 0.6526 (mt-10) cc_final: 0.5806 (tm-30) REVERT: H 51 TYR cc_start: 0.8992 (m-80) cc_final: 0.8785 (m-80) REVERT: H 92 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7664 (m-30) outliers start: 44 outliers final: 24 residues processed: 228 average time/residue: 1.0530 time to fit residues: 268.6431 Evaluate side-chains 204 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 678 GLN Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 172 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN D 678 GLN E 456 GLN E 474 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN F 592 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN H 86 HIS H 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131202 restraints weight = 19924.687| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.65 r_work: 0.3401 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.924 15206 Z= 0.620 Angle : 0.713 45.855 20694 Z= 0.336 Chirality : 0.047 0.687 2113 Planarity : 0.005 0.054 2736 Dihedral : 6.215 74.853 2037 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.50 % Allowed : 10.43 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 1811 helix: -2.99 (0.55), residues: 64 sheet: -0.42 (0.25), residues: 340 loop : -0.64 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 137 HIS 0.012 0.001 HIS F 290 PHE 0.028 0.002 PHE C 629 TYR 0.019 0.002 TYR L 72 ARG 0.005 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 277) hydrogen bonds : angle 6.02155 ( 768) SS BOND : bond 0.00758 ( 2) SS BOND : angle 0.63307 ( 4) covalent geometry : bond 0.01667 (15204) covalent geometry : angle 0.71346 (20690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 1.505 Fit side-chains REVERT: A 412 GLN cc_start: 0.7878 (pt0) cc_final: 0.6843 (tp40) REVERT: A 519 ASN cc_start: 0.7312 (t0) cc_final: 0.7060 (t0) REVERT: A 557 LYS cc_start: 0.6993 (mptt) cc_final: 0.6523 (tptp) REVERT: C 564 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6692 (pm20) REVERT: C 622 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7681 (mm) REVERT: C 725 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8079 (ptp-110) REVERT: D 358 SER cc_start: 0.6870 (m) cc_final: 0.6341 (t) REVERT: D 641 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8420 (mttp) REVERT: E 610 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.4677 (mpt180) REVERT: F 233 GLN cc_start: 0.8075 (mt0) cc_final: 0.7694 (tt0) REVERT: F 312 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7524 (mtm110) REVERT: F 425 SER cc_start: 0.8847 (p) cc_final: 0.8494 (t) REVERT: F 551 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: F 725 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8596 (ptt180) REVERT: L 55 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.3913 (p90) REVERT: L 68 ARG cc_start: 0.6154 (mtm180) cc_final: 0.5606 (ttp-170) outliers start: 56 outliers final: 29 residues processed: 233 average time/residue: 1.0973 time to fit residues: 284.4299 Evaluate side-chains 208 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 102 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN C 255 HIS C 262 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN F 314 ASN F 321 GLN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 86 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128703 restraints weight = 20187.855| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.74 r_work: 0.3368 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.925 15206 Z= 0.637 Angle : 0.747 45.889 20694 Z= 0.356 Chirality : 0.048 0.689 2113 Planarity : 0.005 0.055 2736 Dihedral : 6.313 76.050 2036 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.94 % Allowed : 11.12 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.19 (0.18), residues: 1811 helix: -3.07 (0.55), residues: 64 sheet: -0.67 (0.26), residues: 340 loop : -0.73 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 509 HIS 0.012 0.002 HIS F 290 PHE 0.025 0.002 PHE C 629 TYR 0.024 0.002 TYR F 701 ARG 0.007 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 277) hydrogen bonds : angle 6.15287 ( 768) SS BOND : bond 0.00785 ( 2) SS BOND : angle 0.55266 ( 4) covalent geometry : bond 0.01704 (15204) covalent geometry : angle 0.74657 (20690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 182 time to evaluate : 1.633 Fit side-chains REVERT: A 412 GLN cc_start: 0.7838 (pt0) cc_final: 0.6782 (tp40) REVERT: A 519 ASN cc_start: 0.7468 (t0) cc_final: 0.7190 (t0) REVERT: A 557 LYS cc_start: 0.6959 (mptt) cc_final: 0.6461 (tptp) REVERT: C 564 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: C 622 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7787 (mm) REVERT: C 725 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8060 (ptp-110) REVERT: D 358 SER cc_start: 0.7011 (m) cc_final: 0.6372 (t) REVERT: D 641 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8360 (mttp) REVERT: E 610 ARG cc_start: 0.7027 (ttm-80) cc_final: 0.4607 (mpt180) REVERT: F 233 GLN cc_start: 0.8078 (mt0) cc_final: 0.7623 (tt0) REVERT: F 725 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8614 (ptt180) REVERT: L 55 TYR cc_start: 0.5826 (OUTLIER) cc_final: 0.3848 (p90) REVERT: L 68 ARG cc_start: 0.6314 (mtm180) cc_final: 0.5707 (ttp-170) outliers start: 63 outliers final: 28 residues processed: 225 average time/residue: 1.1511 time to fit residues: 287.8524 Evaluate side-chains 200 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 7.9990 chunk 163 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A 546 GLN B 608 GLN C 262 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN H 22 GLN H 86 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133327 restraints weight = 20142.513| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.66 r_work: 0.3383 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.915 15206 Z= 0.606 Angle : 0.699 52.727 20694 Z= 0.315 Chirality : 0.047 0.973 2113 Planarity : 0.004 0.045 2736 Dihedral : 5.875 75.825 2036 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.50 % Allowed : 13.30 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 1811 helix: -2.91 (0.57), residues: 64 sheet: -0.42 (0.27), residues: 325 loop : -0.64 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 228 HIS 0.003 0.001 HIS C 290 PHE 0.022 0.002 PHE L 106 TYR 0.014 0.001 TYR F 443 ARG 0.005 0.000 ARG L 77 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 277) hydrogen bonds : angle 5.68442 ( 768) SS BOND : bond 0.00770 ( 2) SS BOND : angle 0.49964 ( 4) covalent geometry : bond 0.01633 (15204) covalent geometry : angle 0.69903 (20690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.632 Fit side-chains REVERT: A 265 SER cc_start: 0.7407 (t) cc_final: 0.6871 (m) REVERT: A 412 GLN cc_start: 0.7845 (pt0) cc_final: 0.6806 (tp40) REVERT: A 557 LYS cc_start: 0.6984 (mptt) cc_final: 0.6512 (tptp) REVERT: C 564 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.6659 (pm20) REVERT: C 622 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7694 (mm) REVERT: C 725 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8113 (ptp-110) REVERT: D 358 SER cc_start: 0.6892 (m) cc_final: 0.6316 (t) REVERT: D 565 GLU cc_start: 0.6897 (mp0) cc_final: 0.4883 (pt0) REVERT: D 641 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8434 (mttp) REVERT: E 610 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.4662 (mpt180) REVERT: F 233 GLN cc_start: 0.8137 (mt0) cc_final: 0.7768 (tt0) REVERT: F 425 SER cc_start: 0.8798 (t) cc_final: 0.8493 (t) REVERT: F 725 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8608 (ptt180) REVERT: L 68 ARG cc_start: 0.6079 (mtm180) cc_final: 0.5591 (ttp-170) REVERT: H 103 ASP cc_start: 0.8751 (m-30) cc_final: 0.8465 (m-30) REVERT: H 106 ARG cc_start: 0.8401 (mtm180) cc_final: 0.7802 (mpp-170) outliers start: 40 outliers final: 19 residues processed: 215 average time/residue: 1.1830 time to fit residues: 281.8592 Evaluate side-chains 201 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 608 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 80 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN F 314 ASN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130151 restraints weight = 20120.269| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.74 r_work: 0.3385 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.912 15206 Z= 0.621 Angle : 0.726 51.403 20694 Z= 0.335 Chirality : 0.048 0.946 2113 Planarity : 0.005 0.046 2736 Dihedral : 5.875 75.787 2033 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.06 % Allowed : 13.24 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.07 (0.18), residues: 1811 helix: -2.93 (0.56), residues: 64 sheet: -0.42 (0.27), residues: 325 loop : -0.70 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 509 HIS 0.005 0.001 HIS C 290 PHE 0.028 0.002 PHE L 106 TYR 0.019 0.002 TYR F 701 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 277) hydrogen bonds : angle 5.81357 ( 768) SS BOND : bond 0.00748 ( 2) SS BOND : angle 0.43505 ( 4) covalent geometry : bond 0.01663 (15204) covalent geometry : angle 0.72633 (20690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7445 (t) cc_final: 0.6906 (m) REVERT: A 412 GLN cc_start: 0.7824 (pt0) cc_final: 0.6781 (tp40) REVERT: A 557 LYS cc_start: 0.6923 (mptt) cc_final: 0.6373 (tptp) REVERT: C 564 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: C 622 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7735 (mm) REVERT: C 725 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8060 (ptp-110) REVERT: D 358 SER cc_start: 0.6984 (m) cc_final: 0.6338 (t) REVERT: D 641 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8418 (mttp) REVERT: D 671 ILE cc_start: 0.8087 (pp) cc_final: 0.7780 (pt) REVERT: E 610 ARG cc_start: 0.6979 (ttm-80) cc_final: 0.4589 (mpt180) REVERT: F 233 GLN cc_start: 0.8104 (mt0) cc_final: 0.7728 (tt0) REVERT: F 425 SER cc_start: 0.8731 (t) cc_final: 0.8473 (t) REVERT: F 725 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8607 (ptt180) REVERT: L 68 ARG cc_start: 0.6191 (mtm180) cc_final: 0.5625 (ttp-170) REVERT: H 106 ARG cc_start: 0.8378 (mtm180) cc_final: 0.7874 (mpp-170) outliers start: 49 outliers final: 25 residues processed: 214 average time/residue: 1.2429 time to fit residues: 295.4994 Evaluate side-chains 201 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 94 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 452 ASN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132953 restraints weight = 20135.765| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.60 r_work: 0.3387 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.911 15206 Z= 0.612 Angle : 0.710 52.027 20694 Z= 0.322 Chirality : 0.047 0.943 2113 Planarity : 0.005 0.044 2736 Dihedral : 5.718 74.500 2033 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.75 % Allowed : 13.68 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.18), residues: 1811 helix: -2.82 (0.58), residues: 64 sheet: -0.35 (0.27), residues: 314 loop : -0.70 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 509 HIS 0.004 0.001 HIS C 290 PHE 0.028 0.002 PHE L 106 TYR 0.016 0.002 TYR F 443 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 277) hydrogen bonds : angle 5.66959 ( 768) SS BOND : bond 0.00717 ( 2) SS BOND : angle 0.51233 ( 4) covalent geometry : bond 0.01643 (15204) covalent geometry : angle 0.71011 (20690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7540 (t) cc_final: 0.6985 (m) REVERT: A 412 GLN cc_start: 0.7838 (pt0) cc_final: 0.6844 (tp40) REVERT: A 557 LYS cc_start: 0.6908 (mptt) cc_final: 0.6429 (tptp) REVERT: C 622 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7713 (mm) REVERT: C 725 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8137 (ptp-110) REVERT: D 358 SER cc_start: 0.6977 (m) cc_final: 0.6382 (t) REVERT: D 565 GLU cc_start: 0.6971 (pm20) cc_final: 0.4477 (pt0) REVERT: D 641 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8426 (mttp) REVERT: D 671 ILE cc_start: 0.8116 (pp) cc_final: 0.7824 (pt) REVERT: E 610 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.4640 (mpt180) REVERT: F 233 GLN cc_start: 0.8107 (mt0) cc_final: 0.7746 (tt0) REVERT: F 425 SER cc_start: 0.8771 (t) cc_final: 0.8554 (t) REVERT: F 725 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8591 (ptt180) REVERT: L 68 ARG cc_start: 0.6122 (mtm180) cc_final: 0.5573 (ttp-170) REVERT: L 102 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: H 92 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7738 (m-30) outliers start: 44 outliers final: 25 residues processed: 215 average time/residue: 1.1449 time to fit residues: 273.2036 Evaluate side-chains 200 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 135 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 155 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 HIS H 101 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131986 restraints weight = 20088.975| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.66 r_work: 0.3396 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.914 15206 Z= 0.615 Angle : 0.718 51.989 20694 Z= 0.327 Chirality : 0.048 0.934 2113 Planarity : 0.005 0.045 2736 Dihedral : 5.562 75.307 2030 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.94 % Allowed : 13.55 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.06 (0.18), residues: 1811 helix: -2.83 (0.57), residues: 64 sheet: -0.38 (0.27), residues: 324 loop : -0.70 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 509 HIS 0.005 0.001 HIS C 290 PHE 0.028 0.002 PHE L 106 TYR 0.017 0.002 TYR F 701 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 277) hydrogen bonds : angle 5.72675 ( 768) SS BOND : bond 0.00716 ( 2) SS BOND : angle 0.54509 ( 4) covalent geometry : bond 0.01651 (15204) covalent geometry : angle 0.71841 (20690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7549 (t) cc_final: 0.6987 (m) REVERT: A 412 GLN cc_start: 0.7796 (pt0) cc_final: 0.6798 (tp40) REVERT: A 557 LYS cc_start: 0.6864 (mptt) cc_final: 0.6371 (tptp) REVERT: C 622 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7708 (mm) REVERT: C 725 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8075 (ptp-110) REVERT: D 358 SER cc_start: 0.6998 (m) cc_final: 0.6385 (t) REVERT: D 641 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8422 (mttp) REVERT: D 671 ILE cc_start: 0.8086 (pp) cc_final: 0.7836 (pt) REVERT: E 610 ARG cc_start: 0.7022 (ttm-80) cc_final: 0.4628 (mpt180) REVERT: F 233 GLN cc_start: 0.8116 (mt0) cc_final: 0.7760 (tt0) REVERT: F 425 SER cc_start: 0.8758 (t) cc_final: 0.8550 (t) REVERT: F 725 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8588 (ptt180) REVERT: L 68 ARG cc_start: 0.6088 (mtm180) cc_final: 0.5553 (ttp-170) REVERT: L 102 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: H 92 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7706 (m-30) outliers start: 47 outliers final: 30 residues processed: 212 average time/residue: 1.1063 time to fit residues: 260.8298 Evaluate side-chains 206 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 128 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 608 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN F 314 ASN F 452 ASN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134065 restraints weight = 20049.450| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.60 r_work: 0.3412 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.917 15206 Z= 0.608 Angle : 0.704 52.190 20694 Z= 0.317 Chirality : 0.047 0.928 2113 Planarity : 0.004 0.041 2736 Dihedral : 5.376 74.835 2030 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.19 % Allowed : 14.80 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.18), residues: 1811 helix: -2.75 (0.58), residues: 64 sheet: -0.34 (0.27), residues: 324 loop : -0.67 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 503 HIS 0.004 0.001 HIS C 290 PHE 0.027 0.002 PHE L 106 TYR 0.014 0.002 TYR F 443 ARG 0.010 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 277) hydrogen bonds : angle 5.53195 ( 768) SS BOND : bond 0.00741 ( 2) SS BOND : angle 0.40880 ( 4) covalent geometry : bond 0.01636 (15204) covalent geometry : angle 0.70365 (20690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7513 (t) cc_final: 0.6948 (m) REVERT: A 412 GLN cc_start: 0.7772 (pt0) cc_final: 0.6720 (tp40) REVERT: A 557 LYS cc_start: 0.6818 (mptt) cc_final: 0.6326 (tptp) REVERT: C 622 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7645 (mm) REVERT: C 725 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8056 (ptp-110) REVERT: D 358 SER cc_start: 0.6943 (m) cc_final: 0.6283 (t) REVERT: D 565 GLU cc_start: 0.6982 (pm20) cc_final: 0.4475 (pt0) REVERT: D 641 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8401 (mttp) REVERT: D 671 ILE cc_start: 0.8051 (pp) cc_final: 0.7805 (pt) REVERT: E 610 ARG cc_start: 0.7020 (ttm-80) cc_final: 0.4612 (mpt180) REVERT: F 233 GLN cc_start: 0.8095 (mt0) cc_final: 0.7763 (tt0) REVERT: F 425 SER cc_start: 0.8745 (t) cc_final: 0.8530 (t) REVERT: F 725 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (ptt180) REVERT: L 32 THR cc_start: 0.4629 (OUTLIER) cc_final: 0.4299 (t) REVERT: L 68 ARG cc_start: 0.6108 (mtm180) cc_final: 0.5591 (ttp-170) REVERT: L 102 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5851 (mp0) REVERT: H 101 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8734 (tm130) REVERT: H 106 ARG cc_start: 0.8333 (mtm180) cc_final: 0.7837 (mpp-170) outliers start: 35 outliers final: 26 residues processed: 208 average time/residue: 1.1159 time to fit residues: 257.4563 Evaluate side-chains 202 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 608 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 556 ASP Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 56 optimal weight: 8.9990 chunk 108 optimal weight: 0.0060 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 608 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133580 restraints weight = 20039.692| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.65 r_work: 0.3395 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.917 15206 Z= 0.608 Angle : 0.702 52.161 20694 Z= 0.316 Chirality : 0.047 0.926 2113 Planarity : 0.004 0.040 2736 Dihedral : 5.308 74.947 2029 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.31 % Allowed : 14.87 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.97 (0.19), residues: 1811 helix: -2.70 (0.59), residues: 64 sheet: -0.31 (0.27), residues: 324 loop : -0.64 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 509 HIS 0.004 0.001 HIS C 290 PHE 0.027 0.002 PHE L 106 TYR 0.015 0.002 TYR F 443 ARG 0.009 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 277) hydrogen bonds : angle 5.49457 ( 768) SS BOND : bond 0.00708 ( 2) SS BOND : angle 0.39779 ( 4) covalent geometry : bond 0.01636 (15204) covalent geometry : angle 0.70242 (20690) =============================================================================== Job complete usr+sys time: 9733.47 seconds wall clock time: 168 minutes 21.59 seconds (10101.59 seconds total)