Starting phenix.real_space_refine on Thu Sep 18 05:22:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7p_44319/09_2025/9b7p_44319.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7p_44319/09_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_44319/09_2025/9b7p_44319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7p_44319/09_2025/9b7p_44319.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7p_44319/09_2025/9b7p_44319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7p_44319/09_2025/9b7p_44319.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.80, per 1000 atoms: 0.26 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: 1.22 Conformation dependent library (CDL) restraints added in 685.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.69 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: 2.60 Time building geometry restraints manager: 1.53 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.300 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (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 ARG 0.008 0.001 ARG C 730 TYR 0.029 0.003 TYR F 443 PHE 0.031 0.003 PHE L 106 TRP 0.031 0.002 TRP H 137 HIS 0.014 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.01715 (15204) covalent geometry : angle 0.98574 (20690) SS BOND : bond 0.00440 ( 2) SS BOND : angle 0.84736 ( 4) hydrogen bonds : bond 0.24756 ( 277) hydrogen bonds : angle 9.79154 ( 768) *********************** 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 : 0.585 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: 0.5305 time to fit residues: 200.3040 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 : 0.579 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 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 D 678 GLN E 456 GLN E 474 GLN ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 GLN F 229 HIS F 314 ASN 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133013 restraints weight = 19974.797| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.66 r_work: 0.3387 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.928 15206 Z= 0.624 Angle : 0.759 45.241 20694 Z= 0.368 Chirality : 0.048 0.680 2113 Planarity : 0.005 0.042 2736 Dihedral : 6.718 80.046 2046 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.23 % Rotamer: Outliers : 2.87 % Allowed : 8.24 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 1811 helix: -3.38 (0.48), residues: 64 sheet: -0.78 (0.23), residues: 361 loop : -0.70 (0.14), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 485 TYR 0.022 0.002 TYR F 443 PHE 0.026 0.002 PHE L 106 TRP 0.016 0.002 TRP H 137 HIS 0.013 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.01672 (15204) covalent geometry : angle 0.75869 (20690) SS BOND : bond 0.00771 ( 2) SS BOND : angle 0.46224 ( 4) hydrogen bonds : bond 0.03924 ( 277) hydrogen bonds : angle 6.73258 ( 768) *********************** 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 255 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.597 Fit side-chains REVERT: A 254 ASN cc_start: 0.7712 (m-40) cc_final: 0.7196 (t0) REVERT: A 412 GLN cc_start: 0.7860 (pt0) cc_final: 0.6964 (tp40) REVERT: A 519 ASN cc_start: 0.7330 (t0) cc_final: 0.7042 (t0) REVERT: A 557 LYS cc_start: 0.7074 (mptt) cc_final: 0.6584 (tptp) REVERT: A 641 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8154 (mttm) REVERT: C 312 ARG cc_start: 0.7466 (mtt90) cc_final: 0.7197 (ptt90) REVERT: C 564 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: C 678 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6117 (mt0) REVERT: C 725 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8067 (ptp-110) REVERT: D 358 SER cc_start: 0.6849 (m) cc_final: 0.6373 (t) REVERT: D 641 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8294 (mttp) REVERT: E 610 ARG cc_start: 0.7191 (ttm-80) cc_final: 0.4786 (mpt180) REVERT: F 229 HIS cc_start: 0.7347 (m-70) cc_final: 0.7023 (m-70) REVERT: F 281 TRP cc_start: 0.7094 (m100) cc_final: 0.6145 (m-90) REVERT: L 55 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.4425 (p90) REVERT: L 94 PHE cc_start: 0.7021 (m-80) cc_final: 0.6789 (m-80) REVERT: L 102 GLU cc_start: 0.6624 (mt-10) cc_final: 0.5814 (tm-30) REVERT: H 22 GLN cc_start: 0.6636 (tp40) cc_final: 0.6407 (tp-100) outliers start: 46 outliers final: 15 residues processed: 241 average time/residue: 0.5711 time to fit residues: 152.7740 Evaluate side-chains 195 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 F residue 625 THR 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 H residue 49 SER Chi-restraints excluded: chain H residue 94 SER 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 56 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 0.0370 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN E 456 GLN E 474 GLN F 314 ASN F 452 ASN F 570 ASN F 585 GLN F 592 GLN L 60 GLN L 113 GLN H 86 HIS H 96 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130539 restraints weight = 20241.016| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.75 r_work: 0.3389 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2119 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= 0.625 Angle : 0.733 45.512 20694 Z= 0.350 Chirality : 0.047 0.676 2113 Planarity : 0.005 0.042 2736 Dihedral : 6.474 77.123 2038 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 9.81 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 1811 helix: -3.14 (0.52), residues: 64 sheet: -0.55 (0.25), residues: 340 loop : -0.68 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 485 TYR 0.021 0.002 TYR F 701 PHE 0.027 0.002 PHE C 629 TRP 0.014 0.002 TRP H 137 HIS 0.013 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.01678 (15204) covalent geometry : angle 0.73319 (20690) SS BOND : bond 0.00794 ( 2) SS BOND : angle 0.75777 ( 4) hydrogen bonds : bond 0.03702 ( 277) hydrogen bonds : angle 6.37410 ( 768) *********************** 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 245 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.613 Fit side-chains REVERT: A 254 ASN cc_start: 0.7719 (m-40) cc_final: 0.7198 (t0) REVERT: A 412 GLN cc_start: 0.7893 (pt0) cc_final: 0.6897 (tp40) REVERT: A 519 ASN cc_start: 0.7431 (t0) cc_final: 0.7183 (t0) REVERT: A 557 LYS cc_start: 0.6993 (mptt) cc_final: 0.6480 (tptp) REVERT: C 564 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: C 678 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: C 725 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8060 (ptp-110) REVERT: D 358 SER cc_start: 0.6871 (m) cc_final: 0.6289 (t) REVERT: D 641 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8382 (mttp) REVERT: E 610 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.4661 (mpt180) REVERT: F 233 GLN cc_start: 0.8109 (mt0) cc_final: 0.7565 (tt0) REVERT: F 425 SER cc_start: 0.8882 (p) cc_final: 0.8430 (t) REVERT: F 551 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: L 55 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.4026 (p90) REVERT: L 102 GLU cc_start: 0.6572 (mt-10) cc_final: 0.5841 (tm-30) outliers start: 50 outliers final: 26 residues processed: 230 average time/residue: 0.5742 time to fit residues: 146.4593 Evaluate side-chains 205 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 A residue 657 ASP 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 551 ASP Chi-restraints excluded: chain F residue 553 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 140 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN C 255 HIS C 262 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN E 456 GLN E 474 GLN F 314 ASN F 321 GLN F 585 GLN F 592 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN L 113 GLN H 22 GLN H 86 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128866 restraints weight = 20145.222| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.75 r_work: 0.3368 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2470 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= 0.633 Angle : 0.746 45.874 20694 Z= 0.356 Chirality : 0.048 0.693 2113 Planarity : 0.005 0.060 2736 Dihedral : 6.397 76.375 2037 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.06 % Allowed : 10.37 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.18), residues: 1811 helix: -3.12 (0.54), residues: 64 sheet: -0.66 (0.26), residues: 334 loop : -0.74 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 485 TYR 0.023 0.002 TYR F 701 PHE 0.025 0.002 PHE C 629 TRP 0.014 0.002 TRP D 509 HIS 0.014 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.01694 (15204) covalent geometry : angle 0.74642 (20690) SS BOND : bond 0.00793 ( 2) SS BOND : angle 0.61108 ( 4) hydrogen bonds : bond 0.03528 ( 277) hydrogen bonds : angle 6.20433 ( 768) *********************** 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 254 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.623 Fit side-chains REVERT: A 412 GLN cc_start: 0.7866 (pt0) cc_final: 0.6807 (tp40) REVERT: A 519 ASN cc_start: 0.7460 (t0) cc_final: 0.7155 (t0) REVERT: A 557 LYS cc_start: 0.6975 (mptt) cc_final: 0.6470 (tptp) REVERT: C 564 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: C 725 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8047 (ptp-110) REVERT: D 358 SER cc_start: 0.6955 (m) cc_final: 0.6343 (t) REVERT: D 641 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8346 (mttp) REVERT: E 610 ARG cc_start: 0.7022 (ttm-80) cc_final: 0.4606 (mpt180) REVERT: F 233 GLN cc_start: 0.8085 (mt0) cc_final: 0.7620 (tt0) REVERT: F 425 SER cc_start: 0.8878 (p) cc_final: 0.8531 (t) REVERT: F 551 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: L 55 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.3934 (p90) REVERT: L 68 ARG cc_start: 0.6273 (mtm180) cc_final: 0.5645 (ttp-170) REVERT: H 90 SER cc_start: 0.9099 (p) cc_final: 0.8898 (t) outliers start: 65 outliers final: 30 residues processed: 232 average time/residue: 0.5838 time to fit residues: 149.7559 Evaluate side-chains 203 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 564 GLU 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 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 314 ASN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 110 optimal weight: 10.0000 chunk 11 optimal weight: 0.0270 chunk 153 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 585 GLN F 592 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN L 61 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 58 GLN H 86 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133344 restraints weight = 20091.913| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.71 r_work: 0.3376 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.924 15206 Z= 0.607 Angle : 0.678 46.109 20694 Z= 0.313 Chirality : 0.044 0.669 2113 Planarity : 0.004 0.047 2736 Dihedral : 5.918 73.356 2037 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.87 % Allowed : 12.05 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 1811 helix: -2.94 (0.57), residues: 64 sheet: -0.46 (0.26), residues: 339 loop : -0.62 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.014 0.001 TYR F 443 PHE 0.023 0.002 PHE C 629 TRP 0.011 0.001 TRP C 509 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01639 (15204) covalent geometry : angle 0.67765 (20690) SS BOND : bond 0.00777 ( 2) SS BOND : angle 0.50571 ( 4) hydrogen bonds : bond 0.02894 ( 277) hydrogen bonds : angle 5.79175 ( 768) *********************** 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 243 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.661 Fit side-chains REVERT: A 265 SER cc_start: 0.7415 (t) cc_final: 0.6947 (m) REVERT: A 412 GLN cc_start: 0.7865 (pt0) cc_final: 0.6851 (tp40) REVERT: A 557 LYS cc_start: 0.7011 (mptt) cc_final: 0.6532 (tptp) REVERT: C 564 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: C 622 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7672 (mm) REVERT: C 725 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8072 (ptp-110) REVERT: D 358 SER cc_start: 0.6925 (m) cc_final: 0.6348 (t) REVERT: D 565 GLU cc_start: 0.6927 (mp0) cc_final: 0.4909 (pt0) REVERT: D 641 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8449 (mttp) REVERT: E 610 ARG cc_start: 0.7046 (ttm-80) cc_final: 0.4636 (mpt180) REVERT: F 233 GLN cc_start: 0.8127 (mt0) cc_final: 0.7756 (tt0) REVERT: F 361 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: F 425 SER cc_start: 0.8847 (p) cc_final: 0.8549 (t) REVERT: F 551 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: L 68 ARG cc_start: 0.6104 (mtm180) cc_final: 0.5578 (ttp-170) REVERT: H 90 SER cc_start: 0.9037 (p) cc_final: 0.8831 (t) REVERT: H 106 ARG cc_start: 0.8576 (mtm180) cc_final: 0.7980 (mpp-170) outliers start: 46 outliers final: 17 residues processed: 229 average time/residue: 0.5596 time to fit residues: 141.7435 Evaluate side-chains 200 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 MET 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 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 361 GLU Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 625 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 140 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 147 optimal weight: 0.0980 chunk 24 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 101 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS 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 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 = 0.3776 r_free = 0.3776 target = 0.154627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131901 restraints weight = 19977.038| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.67 r_work: 0.3363 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.920 15206 Z= 0.620 Angle : 0.729 52.535 20694 Z= 0.335 Chirality : 0.048 0.930 2113 Planarity : 0.005 0.049 2736 Dihedral : 5.929 76.239 2033 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.44 % Allowed : 12.49 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.18), residues: 1811 helix: -2.96 (0.56), residues: 64 sheet: -0.47 (0.26), residues: 349 loop : -0.66 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 312 TYR 0.019 0.002 TYR F 701 PHE 0.025 0.002 PHE L 106 TRP 0.015 0.002 TRP C 509 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01661 (15204) covalent geometry : angle 0.72922 (20690) SS BOND : bond 0.00760 ( 2) SS BOND : angle 0.53318 ( 4) hydrogen bonds : bond 0.03098 ( 277) hydrogen bonds : angle 5.86932 ( 768) *********************** 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 238 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7501 (t) cc_final: 0.7031 (m) REVERT: A 412 GLN cc_start: 0.7870 (pt0) cc_final: 0.6862 (tp40) REVERT: A 557 LYS cc_start: 0.6999 (mptt) cc_final: 0.6459 (tptp) REVERT: C 312 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6976 (mtt90) REVERT: C 564 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: C 622 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 725 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8117 (ptp-110) REVERT: D 358 SER cc_start: 0.7025 (m) cc_final: 0.6412 (t) REVERT: D 565 GLU cc_start: 0.6921 (mp0) cc_final: 0.4881 (pt0) REVERT: D 641 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8434 (mttp) REVERT: E 610 ARG cc_start: 0.7022 (ttm-80) cc_final: 0.4642 (mpt180) REVERT: F 233 GLN cc_start: 0.8140 (mt0) cc_final: 0.7753 (tt0) REVERT: L 55 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.3588 (p90) REVERT: L 68 ARG cc_start: 0.6142 (mtm180) cc_final: 0.5593 (ttp-170) REVERT: H 106 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8082 (mpp-170) outliers start: 55 outliers final: 31 residues processed: 222 average time/residue: 0.5808 time to fit residues: 142.9418 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 : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 564 GLU 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 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 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 L residue 35 LEU 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 88 THR Chi-restraints excluded: chain H residue 94 SER 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 133 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 84 optimal weight: 0.2980 chunk 98 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 321 GLN 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 = 0.3784 r_free = 0.3784 target = 0.155423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132621 restraints weight = 20020.349| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.66 r_work: 0.3380 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.924 15206 Z= 0.612 Angle : 0.719 53.060 20694 Z= 0.326 Chirality : 0.047 0.883 2113 Planarity : 0.005 0.045 2736 Dihedral : 5.776 75.224 2033 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 12.87 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.18), residues: 1811 helix: -2.91 (0.57), residues: 64 sheet: -0.47 (0.27), residues: 319 loop : -0.67 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 312 TYR 0.016 0.002 TYR F 701 PHE 0.021 0.002 PHE L 106 TRP 0.012 0.001 TRP D 509 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01644 (15204) covalent geometry : angle 0.71854 (20690) SS BOND : bond 0.00707 ( 2) SS BOND : angle 0.46741 ( 4) hydrogen bonds : bond 0.02904 ( 277) hydrogen bonds : angle 5.74742 ( 768) *********************** 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: 48 poor density : 181 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7519 (t) cc_final: 0.7047 (m) REVERT: A 412 GLN cc_start: 0.7824 (pt0) cc_final: 0.6822 (tp40) REVERT: A 557 LYS cc_start: 0.6915 (mptt) cc_final: 0.6426 (tptp) REVERT: C 312 ARG cc_start: 0.7321 (mtm110) cc_final: 0.7020 (mtt90) REVERT: C 564 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: C 622 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7703 (mm) REVERT: C 725 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8097 (ptp-110) REVERT: D 358 SER cc_start: 0.7009 (m) cc_final: 0.6413 (t) REVERT: D 641 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8440 (mttp) REVERT: E 610 ARG cc_start: 0.6974 (ttm-80) cc_final: 0.4619 (mpt180) REVERT: F 233 GLN cc_start: 0.8112 (mt0) cc_final: 0.7745 (tt0) REVERT: F 425 SER cc_start: 0.8806 (t) cc_final: 0.8486 (t) REVERT: L 68 ARG cc_start: 0.6145 (mtm180) cc_final: 0.5605 (ttp-170) REVERT: L 102 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6002 (tm-30) REVERT: H 92 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: H 106 ARG cc_start: 0.8556 (mtm180) cc_final: 0.8096 (mpp-170) outliers start: 48 outliers final: 27 residues processed: 217 average time/residue: 0.5812 time to fit residues: 139.2623 Evaluate side-chains 201 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 457 ASN Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain L residue 24 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 0.0030 chunk 165 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 overall best weight: 6.1998 ------------------------------------------------------------------------------- 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 456 GLN C 585 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN E 474 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129840 restraints weight = 20246.353| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.66 r_work: 0.3339 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2898 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= 0.643 Angle : 0.781 52.714 20694 Z= 0.366 Chirality : 0.051 0.914 2113 Planarity : 0.005 0.053 2736 Dihedral : 6.162 78.966 2033 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.00 % Allowed : 13.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.18), residues: 1811 helix: -3.06 (0.55), residues: 64 sheet: -0.66 (0.27), residues: 329 loop : -0.82 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 312 TYR 0.025 0.003 TYR F 701 PHE 0.025 0.003 PHE C 629 TRP 0.016 0.002 TRP D 509 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01711 (15204) covalent geometry : angle 0.78066 (20690) SS BOND : bond 0.00768 ( 2) SS BOND : angle 0.54176 ( 4) hydrogen bonds : bond 0.03491 ( 277) hydrogen bonds : angle 6.15306 ( 768) *********************** 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 225 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.7876 (pt0) cc_final: 0.6855 (tp40) REVERT: A 557 LYS cc_start: 0.6956 (mptt) cc_final: 0.6427 (tptp) REVERT: C 312 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7140 (mtm110) REVERT: C 564 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: C 622 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7724 (mm) REVERT: C 725 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (ptp-110) REVERT: D 358 SER cc_start: 0.7171 (m) cc_final: 0.6512 (t) REVERT: D 565 GLU cc_start: 0.7075 (pm20) cc_final: 0.4565 (pt0) REVERT: D 641 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8385 (mttp) REVERT: D 671 ILE cc_start: 0.8229 (pp) cc_final: 0.8002 (pt) REVERT: E 610 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.4656 (mpt180) REVERT: F 233 GLN cc_start: 0.8201 (mt0) cc_final: 0.7793 (tt0) REVERT: F 425 SER cc_start: 0.8772 (t) cc_final: 0.8523 (t) REVERT: L 68 ARG cc_start: 0.6231 (mtm180) cc_final: 0.5713 (ttp-170) REVERT: L 102 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5962 (tm-30) REVERT: H 106 ARG cc_start: 0.8499 (mtm180) cc_final: 0.7928 (mpp-170) outliers start: 48 outliers final: 28 residues processed: 211 average time/residue: 0.5704 time to fit residues: 132.8346 Evaluate side-chains 197 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 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 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 88 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 84 optimal weight: 0.4980 chunk 116 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 67 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 135 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- 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 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 = 0.3780 r_free = 0.3780 target = 0.155098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132406 restraints weight = 20147.044| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.66 r_work: 0.3382 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.924 15206 Z= 0.610 Angle : 0.724 52.654 20694 Z= 0.330 Chirality : 0.047 0.890 2113 Planarity : 0.005 0.047 2736 Dihedral : 5.845 76.394 2033 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.44 % Allowed : 13.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.18), residues: 1811 helix: -2.95 (0.56), residues: 64 sheet: -0.49 (0.27), residues: 325 loop : -0.75 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.015 0.002 TYR F 443 PHE 0.023 0.002 PHE L 106 TRP 0.014 0.001 TRP B 607 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01641 (15204) covalent geometry : angle 0.72433 (20690) SS BOND : bond 0.00763 ( 2) SS BOND : angle 0.46192 ( 4) hydrogen bonds : bond 0.02946 ( 277) hydrogen bonds : angle 5.82104 ( 768) *********************** 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 217 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.7860 (pt0) cc_final: 0.6853 (tp40) REVERT: A 557 LYS cc_start: 0.6924 (mptt) cc_final: 0.6403 (tptp) REVERT: C 312 ARG cc_start: 0.7335 (mtm110) cc_final: 0.7031 (mtt90) REVERT: C 564 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: C 622 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7686 (mm) REVERT: C 725 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8105 (ptp-110) REVERT: D 358 SER cc_start: 0.7036 (m) cc_final: 0.6396 (t) REVERT: D 565 GLU cc_start: 0.7072 (pm20) cc_final: 0.4572 (pt0) REVERT: D 641 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8415 (mttp) REVERT: D 671 ILE cc_start: 0.8190 (pp) cc_final: 0.7953 (pt) REVERT: E 610 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.4667 (mpt180) REVERT: F 233 GLN cc_start: 0.8141 (mt0) cc_final: 0.7781 (tt0) REVERT: F 425 SER cc_start: 0.8811 (t) cc_final: 0.8548 (t) REVERT: L 55 TYR cc_start: 0.5809 (OUTLIER) cc_final: 0.3387 (p90) REVERT: L 68 ARG cc_start: 0.6165 (mtm180) cc_final: 0.5599 (ttp-170) REVERT: L 102 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6045 (tm-30) REVERT: H 106 ARG cc_start: 0.8429 (mtm180) cc_final: 0.7901 (mpp-170) outliers start: 39 outliers final: 28 residues processed: 208 average time/residue: 0.6069 time to fit residues: 139.3169 Evaluate side-chains 202 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 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 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 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 141 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 149 optimal weight: 0.3980 chunk 164 optimal weight: 20.0000 chunk 101 optimal weight: 0.0770 chunk 89 optimal weight: 9.9990 overall best weight: 2.8944 ------------------------------------------------------------------------------- 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 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 = 0.3779 r_free = 0.3779 target = 0.155132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132470 restraints weight = 20031.805| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.66 r_work: 0.3378 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.927 15206 Z= 0.612 Angle : 0.723 52.758 20694 Z= 0.328 Chirality : 0.047 0.884 2113 Planarity : 0.005 0.045 2736 Dihedral : 5.725 75.877 2033 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.19 % Allowed : 14.43 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.18), residues: 1811 helix: -2.90 (0.57), residues: 64 sheet: -0.43 (0.27), residues: 323 loop : -0.72 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 312 TYR 0.016 0.002 TYR F 701 PHE 0.025 0.002 PHE C 275 TRP 0.011 0.001 TRP D 509 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01645 (15204) covalent geometry : angle 0.72293 (20690) SS BOND : bond 0.00738 ( 2) SS BOND : angle 0.42796 ( 4) hydrogen bonds : bond 0.02895 ( 277) hydrogen bonds : angle 5.71037 ( 768) ********************** 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 211 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 265 SER cc_start: 0.7546 (t) cc_final: 0.6807 (m) REVERT: A 412 GLN cc_start: 0.7873 (pt0) cc_final: 0.6860 (tp40) REVERT: A 557 LYS cc_start: 0.6880 (mptt) cc_final: 0.6394 (tptp) REVERT: C 312 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7068 (mtt90) REVERT: C 564 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: C 622 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 725 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8108 (ptp-110) REVERT: D 358 SER cc_start: 0.7037 (m) cc_final: 0.6407 (t) REVERT: D 641 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8413 (mttp) REVERT: D 671 ILE cc_start: 0.8143 (pp) cc_final: 0.7909 (pt) REVERT: E 610 ARG cc_start: 0.7076 (ttm-80) cc_final: 0.4656 (mpt180) REVERT: F 233 GLN cc_start: 0.8147 (mt0) cc_final: 0.7801 (tt0) REVERT: F 425 SER cc_start: 0.8800 (t) cc_final: 0.8578 (t) REVERT: F 584 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7335 (m170) REVERT: L 55 TYR cc_start: 0.5804 (OUTLIER) cc_final: 0.3284 (p90) REVERT: L 68 ARG cc_start: 0.6109 (mtm180) cc_final: 0.5549 (ttp-170) REVERT: L 102 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6017 (tm-30) REVERT: H 106 ARG cc_start: 0.8463 (mtm180) cc_final: 0.7922 (mpp-170) outliers start: 35 outliers final: 28 residues processed: 204 average time/residue: 0.5893 time to fit residues: 132.8579 Evaluate side-chains 201 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 420 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 584 HIS 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 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 452 ASN F 585 GLN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN ** 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 = 0.3775 r_free = 0.3775 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132020 restraints weight = 20076.240| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.67 r_work: 0.3371 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3006 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= 0.618 Angle : 0.731 52.630 20694 Z= 0.334 Chirality : 0.047 0.895 2113 Planarity : 0.005 0.045 2736 Dihedral : 5.752 76.367 2033 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.25 % Allowed : 14.30 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.18), residues: 1811 helix: -2.92 (0.56), residues: 64 sheet: -0.43 (0.27), residues: 323 loop : -0.74 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 312 TYR 0.018 0.002 TYR F 701 PHE 0.022 0.002 PHE L 106 TRP 0.012 0.002 TRP D 509 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.01657 (15204) covalent geometry : angle 0.73086 (20690) SS BOND : bond 0.00733 ( 2) SS BOND : angle 0.42739 ( 4) hydrogen bonds : bond 0.02985 ( 277) hydrogen bonds : angle 5.73576 ( 768) =============================================================================== Job complete usr+sys time: 5017.40 seconds wall clock time: 86 minutes 26.45 seconds (5186.45 seconds total)