Starting phenix.real_space_refine on Fri Mar 6 01:42:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6okt_20104/03_2026/6okt_20104.cif Found real_map, /net/cci-nas-00/data/ceres_data/6okt_20104/03_2026/6okt_20104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6okt_20104/03_2026/6okt_20104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6okt_20104/03_2026/6okt_20104.map" model { file = "/net/cci-nas-00/data/ceres_data/6okt_20104/03_2026/6okt_20104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6okt_20104/03_2026/6okt_20104.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 42 5.16 5 C 16926 2.51 5 N 4368 2.21 5 O 5712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 1 Chain: "H" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Restraints were copied for chains: I, J, K, L, M, N Time building chain proxies: 3.55, per 1000 atoms: 0.13 Number of scatterers: 27048 At special positions: 0 Unit cell: (181.25, 179.8, 134.85, 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 42 16.00 O 5712 8.00 N 4368 7.00 C 16926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6468 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 64 sheets defined 14.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'H' and resid 226 through 232 Processing helix chain 'H' and resid 272 through 278 removed outlier: 3.836A pdb=" N SER H 278 " --> pdb=" O TYR H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 290 Processing helix chain 'H' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE H 429 " --> pdb=" O GLU H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 472 Processing helix chain 'H' and resid 503 through 505 No H-bonds generated for 'chain 'H' and resid 503 through 505' Processing helix chain 'H' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE H 510 " --> pdb=" O TYR H 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 513 " --> pdb=" O GLN H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 593 removed outlier: 4.037A pdb=" N LYS H 593 " --> pdb=" O LYS H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU H 662 " --> pdb=" O PRO H 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 232 Processing helix chain 'I' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER I 278 " --> pdb=" O TYR I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 290 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE I 429 " --> pdb=" O GLU I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 472 Processing helix chain 'I' and resid 503 through 505 No H-bonds generated for 'chain 'I' and resid 503 through 505' Processing helix chain 'I' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE I 510 " --> pdb=" O TYR I 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE I 513 " --> pdb=" O GLN I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 555 removed outlier: 3.697A pdb=" N PHE I 555 " --> pdb=" O ILE I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 593 removed outlier: 4.037A pdb=" N LYS I 593 " --> pdb=" O LYS I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU I 662 " --> pdb=" O PRO I 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 232 Processing helix chain 'J' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER J 278 " --> pdb=" O TYR J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.712A pdb=" N ILE J 429 " --> pdb=" O GLU J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 463 through 472 Processing helix chain 'J' and resid 503 through 505 No H-bonds generated for 'chain 'J' and resid 503 through 505' Processing helix chain 'J' and resid 506 through 513 removed outlier: 4.143A pdb=" N ILE J 510 " --> pdb=" O TYR J 506 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 513 " --> pdb=" O GLN J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE J 555 " --> pdb=" O ILE J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS J 593 " --> pdb=" O LYS J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU J 662 " --> pdb=" O PRO J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 232 Processing helix chain 'K' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER K 278 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 290 Processing helix chain 'K' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE K 429 " --> pdb=" O GLU K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 472 Processing helix chain 'K' and resid 503 through 505 No H-bonds generated for 'chain 'K' and resid 503 through 505' Processing helix chain 'K' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE K 510 " --> pdb=" O TYR K 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 513 " --> pdb=" O GLN K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE K 555 " --> pdb=" O ILE K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS K 593 " --> pdb=" O LYS K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU K 662 " --> pdb=" O PRO K 659 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 232 Processing helix chain 'L' and resid 272 through 278 removed outlier: 3.836A pdb=" N SER L 278 " --> pdb=" O TYR L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 290 Processing helix chain 'L' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE L 429 " --> pdb=" O GLU L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 472 Processing helix chain 'L' and resid 503 through 505 No H-bonds generated for 'chain 'L' and resid 503 through 505' Processing helix chain 'L' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE L 510 " --> pdb=" O TYR L 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 555 removed outlier: 3.699A pdb=" N PHE L 555 " --> pdb=" O ILE L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS L 593 " --> pdb=" O LYS L 589 " (cutoff:3.500A) Processing helix chain 'L' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU L 662 " --> pdb=" O PRO L 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 232 Processing helix chain 'M' and resid 272 through 278 removed outlier: 3.836A pdb=" N SER M 278 " --> pdb=" O TYR M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE M 429 " --> pdb=" O GLU M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 463 through 472 Processing helix chain 'M' and resid 503 through 505 No H-bonds generated for 'chain 'M' and resid 503 through 505' Processing helix chain 'M' and resid 506 through 513 removed outlier: 4.144A pdb=" N ILE M 510 " --> pdb=" O TYR M 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 513 " --> pdb=" O GLN M 509 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 555 removed outlier: 3.698A pdb=" N PHE M 555 " --> pdb=" O ILE M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS M 593 " --> pdb=" O LYS M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU M 662 " --> pdb=" O PRO M 659 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 232 Processing helix chain 'N' and resid 272 through 278 removed outlier: 3.835A pdb=" N SER N 278 " --> pdb=" O TYR N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 290 Processing helix chain 'N' and resid 425 through 429 removed outlier: 3.711A pdb=" N ILE N 429 " --> pdb=" O GLU N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 472 Processing helix chain 'N' and resid 503 through 505 No H-bonds generated for 'chain 'N' and resid 503 through 505' Processing helix chain 'N' and resid 506 through 513 removed outlier: 4.143A pdb=" N ILE N 510 " --> pdb=" O TYR N 506 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE N 513 " --> pdb=" O GLN N 509 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 555 removed outlier: 3.699A pdb=" N PHE N 555 " --> pdb=" O ILE N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 581 through 593 removed outlier: 4.038A pdb=" N LYS N 593 " --> pdb=" O LYS N 589 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 663 removed outlier: 4.013A pdb=" N GLU N 662 " --> pdb=" O PRO N 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 236 through 238 Processing sheet with id=AA2, first strand: chain 'H' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL H 300 " --> pdb=" O THR H 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR H 398 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 302 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR H 396 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET H 304 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 394 " --> pdb=" O MET H 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS H 306 " --> pdb=" O ASN H 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL H 300 " --> pdb=" O THR H 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR H 398 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 302 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR H 396 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET H 304 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 394 " --> pdb=" O MET H 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS H 306 " --> pdb=" O ASN H 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 314 through 326 removed outlier: 3.687A pdb=" N ASN H 371 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS N 321 " --> pdb=" O TRP H 375 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN N 371 " --> pdb=" O ARG M 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG M 325 " --> pdb=" O ASN N 371 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 323 " --> pdb=" O GLU N 373 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 321 " --> pdb=" O TRP N 375 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN M 371 " --> pdb=" O ARG L 325 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS L 321 " --> pdb=" O TRP M 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE M 381 " --> pdb=" O ALA L 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 315 " --> pdb=" O ILE M 381 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE L 381 " --> pdb=" O ALA K 315 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 315 " --> pdb=" O ILE L 381 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN K 371 " --> pdb=" O ARG J 325 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS J 321 " --> pdb=" O TRP K 375 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN J 371 " --> pdb=" O ARG I 325 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS I 321 " --> pdb=" O TRP J 375 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN I 371 " --> pdb=" O ARG H 325 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS H 321 " --> pdb=" O TRP I 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 420 through 423 removed outlier: 3.813A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL H 406 " --> pdb=" O SER H 484 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER H 484 " --> pdb=" O VAL H 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN H 482 " --> pdb=" O PRO H 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR H 410 " --> pdb=" O THR H 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR H 480 " --> pdb=" O THR H 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 489 through 490 removed outlier: 3.856A pdb=" N THR H 489 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'H' and resid 558 through 560 removed outlier: 3.604A pdb=" N LEU H 564 " --> pdb=" O ILE H 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 618 through 619 Processing sheet with id=AB1, first strand: chain 'H' and resid 651 through 658 removed outlier: 3.745A pdb=" N THR H 680 " --> pdb=" O SER H 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 236 through 238 Processing sheet with id=AB3, first strand: chain 'I' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL I 300 " --> pdb=" O THR I 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR I 398 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 306 " --> pdb=" O ASN I 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL I 300 " --> pdb=" O THR I 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR I 398 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 306 " --> pdb=" O ASN I 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER I 420 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL I 406 " --> pdb=" O SER I 484 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER I 484 " --> pdb=" O VAL I 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN I 482 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR I 410 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR I 480 " --> pdb=" O THR I 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR I 489 " --> pdb=" O VAL I 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 525 through 531 Processing sheet with id=AB8, first strand: chain 'I' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU I 564 " --> pdb=" O ILE I 571 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 618 through 619 Processing sheet with id=AC1, first strand: chain 'I' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR I 680 " --> pdb=" O SER I 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 236 through 238 Processing sheet with id=AC3, first strand: chain 'J' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL J 300 " --> pdb=" O THR J 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR J 398 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 302 " --> pdb=" O TYR J 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR J 396 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS J 306 " --> pdb=" O ASN J 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL J 300 " --> pdb=" O THR J 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR J 398 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 302 " --> pdb=" O TYR J 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR J 396 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS J 306 " --> pdb=" O ASN J 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER J 420 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL J 406 " --> pdb=" O SER J 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER J 484 " --> pdb=" O VAL J 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN J 482 " --> pdb=" O PRO J 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR J 410 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR J 480 " --> pdb=" O THR J 410 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR J 489 " --> pdb=" O VAL J 497 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 525 through 531 Processing sheet with id=AC8, first strand: chain 'J' and resid 558 through 560 removed outlier: 3.602A pdb=" N LEU J 564 " --> pdb=" O ILE J 571 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 618 through 619 Processing sheet with id=AD1, first strand: chain 'J' and resid 651 through 658 removed outlier: 3.745A pdb=" N THR J 680 " --> pdb=" O SER J 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 236 through 238 Processing sheet with id=AD3, first strand: chain 'K' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL K 300 " --> pdb=" O THR K 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR K 398 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS K 306 " --> pdb=" O ASN K 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL K 300 " --> pdb=" O THR K 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR K 398 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS K 306 " --> pdb=" O ASN K 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER K 420 " --> pdb=" O LEU K 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL K 406 " --> pdb=" O SER K 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER K 484 " --> pdb=" O VAL K 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN K 482 " --> pdb=" O PRO K 408 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR K 410 " --> pdb=" O THR K 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR K 480 " --> pdb=" O THR K 410 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR K 489 " --> pdb=" O VAL K 497 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 525 through 531 Processing sheet with id=AD8, first strand: chain 'K' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU K 564 " --> pdb=" O ILE K 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 618 through 619 Processing sheet with id=AE1, first strand: chain 'K' and resid 651 through 658 removed outlier: 3.745A pdb=" N THR K 680 " --> pdb=" O SER K 728 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 236 through 238 Processing sheet with id=AE3, first strand: chain 'L' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL L 300 " --> pdb=" O THR L 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR L 398 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 302 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR L 396 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET L 304 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG L 394 " --> pdb=" O MET L 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 306 " --> pdb=" O ASN L 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL L 300 " --> pdb=" O THR L 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR L 398 " --> pdb=" O VAL L 300 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 302 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR L 396 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET L 304 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG L 394 " --> pdb=" O MET L 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 306 " --> pdb=" O ASN L 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER L 420 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL L 406 " --> pdb=" O SER L 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER L 484 " --> pdb=" O VAL L 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN L 482 " --> pdb=" O PRO L 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR L 410 " --> pdb=" O THR L 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR L 480 " --> pdb=" O THR L 410 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 489 through 490 removed outlier: 3.856A pdb=" N THR L 489 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 525 through 531 Processing sheet with id=AE8, first strand: chain 'L' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU L 564 " --> pdb=" O ILE L 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'L' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR L 680 " --> pdb=" O SER L 728 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 236 through 238 Processing sheet with id=AF3, first strand: chain 'M' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL M 300 " --> pdb=" O THR M 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR M 398 " --> pdb=" O VAL M 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 302 " --> pdb=" O TYR M 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR M 396 " --> pdb=" O VAL M 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 299 through 311 removed outlier: 5.323A pdb=" N VAL M 300 " --> pdb=" O THR M 398 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR M 398 " --> pdb=" O VAL M 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 302 " --> pdb=" O TYR M 396 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR M 396 " --> pdb=" O VAL M 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL M 406 " --> pdb=" O SER M 484 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER M 484 " --> pdb=" O VAL M 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN M 482 " --> pdb=" O PRO M 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR M 410 " --> pdb=" O THR M 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR M 480 " --> pdb=" O THR M 410 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR M 489 " --> pdb=" O VAL M 497 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 525 through 531 Processing sheet with id=AF8, first strand: chain 'M' and resid 558 through 560 removed outlier: 3.604A pdb=" N LEU M 564 " --> pdb=" O ILE M 571 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 618 through 619 Processing sheet with id=AG1, first strand: chain 'M' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR M 680 " --> pdb=" O SER M 728 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 236 through 238 Processing sheet with id=AG3, first strand: chain 'N' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL N 300 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR N 398 " --> pdb=" O VAL N 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL N 302 " --> pdb=" O TYR N 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR N 396 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET N 304 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 394 " --> pdb=" O MET N 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS N 306 " --> pdb=" O ASN N 392 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 299 through 311 removed outlier: 5.322A pdb=" N VAL N 300 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR N 398 " --> pdb=" O VAL N 300 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL N 302 " --> pdb=" O TYR N 396 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR N 396 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET N 304 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 394 " --> pdb=" O MET N 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS N 306 " --> pdb=" O ASN N 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 420 through 423 removed outlier: 3.812A pdb=" N SER N 420 " --> pdb=" O LEU N 412 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL N 406 " --> pdb=" O SER N 484 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER N 484 " --> pdb=" O VAL N 406 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN N 482 " --> pdb=" O PRO N 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR N 410 " --> pdb=" O THR N 480 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR N 480 " --> pdb=" O THR N 410 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 489 through 490 removed outlier: 3.855A pdb=" N THR N 489 " --> pdb=" O VAL N 497 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 525 through 531 Processing sheet with id=AG8, first strand: chain 'N' and resid 558 through 560 removed outlier: 3.603A pdb=" N LEU N 564 " --> pdb=" O ILE N 571 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 618 through 619 Processing sheet with id=AH1, first strand: chain 'N' and resid 651 through 658 removed outlier: 3.744A pdb=" N THR N 680 " --> pdb=" O SER N 728 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2256 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: 5.10 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8597 1.34 - 1.45: 3789 1.45 - 1.57: 15054 1.57 - 1.68: 0 1.68 - 1.80: 77 Bond restraints: 27517 Sorted by residual: bond pdb=" C LYS H 541 " pdb=" N THR H 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.47e+00 bond pdb=" C LYS L 541 " pdb=" N THR L 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.46e+00 bond pdb=" C LYS K 541 " pdb=" N THR K 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.43e+00 bond pdb=" C LYS N 541 " pdb=" N THR N 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.41e+00 bond pdb=" C LYS I 541 " pdb=" N THR I 542 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.37e+00 ... (remaining 27512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 36153 2.36 - 4.73: 1035 4.73 - 7.09: 91 7.09 - 9.46: 24 9.46 - 11.82: 14 Bond angle restraints: 37317 Sorted by residual: angle pdb=" C ARG L 232 " pdb=" N ASN L 233 " pdb=" CA ASN L 233 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C ARG N 232 " pdb=" N ASN N 233 " pdb=" CA ASN N 233 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C ARG H 232 " pdb=" N ASN H 233 " pdb=" CA ASN H 233 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ARG J 232 " pdb=" N ASN J 233 " pdb=" CA ASN J 233 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ARG M 232 " pdb=" N ASN M 233 " pdb=" CA ASN M 233 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 ... (remaining 37312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.89: 13866 13.89 - 27.78: 2052 27.78 - 41.67: 635 41.67 - 55.56: 142 55.56 - 69.46: 70 Dihedral angle restraints: 16765 sinusoidal: 6664 harmonic: 10101 Sorted by residual: dihedral pdb=" CA ASN M 223 " pdb=" C ASN M 223 " pdb=" N ASP M 224 " pdb=" CA ASP M 224 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA ASN L 223 " pdb=" C ASN L 223 " pdb=" N ASP L 224 " pdb=" CA ASP L 224 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA ASN I 223 " pdb=" C ASN I 223 " pdb=" N ASP I 224 " pdb=" CA ASP I 224 " ideal model delta harmonic sigma weight residual 180.00 149.55 30.45 0 5.00e+00 4.00e-02 3.71e+01 ... (remaining 16762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3360 0.069 - 0.138: 760 0.138 - 0.207: 87 0.207 - 0.276: 7 0.276 - 0.345: 7 Chirality restraints: 4221 Sorted by residual: chirality pdb=" CB VAL L 686 " pdb=" CA VAL L 686 " pdb=" CG1 VAL L 686 " pdb=" CG2 VAL L 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL H 686 " pdb=" CA VAL H 686 " pdb=" CG1 VAL H 686 " pdb=" CG2 VAL H 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB VAL M 686 " pdb=" CA VAL M 686 " pdb=" CG1 VAL M 686 " pdb=" CG2 VAL M 686 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 4218 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE L 510 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ILE L 510 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE L 510 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP L 511 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE I 510 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C ILE I 510 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE I 510 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP I 511 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 510 " -0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ILE H 510 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE H 510 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP H 511 " -0.016 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2681 2.73 - 3.27: 25657 3.27 - 3.82: 43681 3.82 - 4.36: 48758 4.36 - 4.90: 84176 Nonbonded interactions: 204953 Sorted by model distance: nonbonded pdb=" O ALA J 315 " pdb=" OG SER K 380 " model vdw 2.188 3.040 nonbonded pdb=" O TYR J 674 " pdb=" OH TYR J 697 " model vdw 2.246 3.040 nonbonded pdb=" O TYR H 674 " pdb=" OH TYR H 697 " model vdw 2.246 3.040 nonbonded pdb=" O TYR K 674 " pdb=" OH TYR K 697 " model vdw 2.246 3.040 nonbonded pdb=" O TYR M 674 " pdb=" OH TYR M 697 " model vdw 2.246 3.040 ... (remaining 204948 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: 0.07 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 0.930 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.110 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.007 0.052 27517 Z= 0.336 Angle : 0.959 11.819 37317 Z= 0.525 Chirality : 0.059 0.345 4221 Planarity : 0.006 0.065 4858 Dihedral : 15.348 69.455 10297 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 1.60 % Allowed : 12.62 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 are not related in a simple way. whole: -4.31 (0.11), residues: 3423 helix: -3.35 (0.15), residues: 441 sheet: -1.65 (0.14), residues: 1008 loop : -3.58 (0.11), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 232 TYR 0.023 0.003 TYR K 261 PHE 0.025 0.003 PHE I 487 TRP 0.009 0.002 TRP N 632 HIS 0.020 0.013 HIS N 314 Details of bonding type rmsd covalent geometry : bond 0.00721 (27517) covalent geometry : angle 0.95860 (37317) hydrogen bonds : bond 0.16388 ( 843) hydrogen bonds : angle 7.23052 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 414 LEU cc_start: 0.8824 (tp) cc_final: 0.8620 (tt) REVERT: H 452 MET cc_start: 0.6164 (ptt) cc_final: 0.5850 (ptt) REVERT: H 539 GLU cc_start: 0.8498 (pp20) cc_final: 0.8057 (tm-30) REVERT: I 736 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7950 (mp) REVERT: J 539 GLU cc_start: 0.8364 (pp20) cc_final: 0.8033 (tm-30) REVERT: J 540 ASP cc_start: 0.8297 (t70) cc_final: 0.8083 (t0) REVERT: J 663 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5569 (pp) REVERT: K 553 LYS cc_start: 0.7802 (tttm) cc_final: 0.7400 (mmtp) REVERT: K 636 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.4803 (p0) REVERT: K 657 LYS cc_start: 0.7987 (mttt) cc_final: 0.7683 (pttt) REVERT: K 736 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7703 (mp) REVERT: M 453 ASP cc_start: 0.9007 (t0) cc_final: 0.8714 (t0) REVERT: M 482 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: M 625 TYR cc_start: 0.7926 (t80) cc_final: 0.7712 (t80) REVERT: M 709 TYR cc_start: 0.8339 (m-80) cc_final: 0.7931 (m-80) REVERT: M 736 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7847 (mp) REVERT: N 386 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8180 (p) REVERT: N 403 MET cc_start: 0.8937 (tpp) cc_final: 0.8516 (ttm) REVERT: N 482 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: N 736 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7754 (mp) outliers start: 49 outliers final: 8 residues processed: 278 average time/residue: 0.1703 time to fit residues: 76.2749 Evaluate side-chains 156 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 648 ASN ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 648 ASN I 720 ASN J 648 ASN ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 454 GLN K 648 ASN ** L 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 648 ASN M 648 ASN N 463 ASN N 648 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087969 restraints weight = 77125.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086737 restraints weight = 74569.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087813 restraints weight = 78683.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.087993 restraints weight = 51284.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088530 restraints weight = 46435.322| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27517 Z= 0.209 Angle : 0.710 8.491 37317 Z= 0.381 Chirality : 0.046 0.168 4221 Planarity : 0.004 0.047 4858 Dihedral : 6.564 26.187 3696 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -3.42 (0.13), residues: 3423 helix: -2.10 (0.21), residues: 406 sheet: -0.98 (0.16), residues: 889 loop : -3.06 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 290 TYR 0.012 0.002 TYR M 261 PHE 0.017 0.002 PHE M 487 TRP 0.010 0.001 TRP J 503 HIS 0.009 0.005 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00446 (27517) covalent geometry : angle 0.71012 (37317) hydrogen bonds : bond 0.04507 ( 843) hydrogen bonds : angle 6.13613 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 452 MET cc_start: 0.6601 (ptt) cc_final: 0.6387 (ptt) REVERT: H 709 TYR cc_start: 0.8374 (m-80) cc_final: 0.8060 (m-10) REVERT: J 380 SER cc_start: 0.8552 (t) cc_final: 0.8214 (m) REVERT: J 452 MET cc_start: 0.6553 (ptt) cc_final: 0.6322 (ptt) REVERT: K 432 ASN cc_start: 0.9396 (m-40) cc_final: 0.9182 (m-40) REVERT: K 660 MET cc_start: 0.6153 (mpp) cc_final: 0.5768 (mpp) REVERT: M 709 TYR cc_start: 0.8749 (m-80) cc_final: 0.8521 (m-10) REVERT: N 403 MET cc_start: 0.8779 (tpp) cc_final: 0.8117 (ttm) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1648 time to fit residues: 61.6987 Evaluate side-chains 153 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 49 optimal weight: 0.0000 chunk 118 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 152 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 214 optimal weight: 0.0170 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 200 optimal weight: 0.2980 chunk 81 optimal weight: 8.9990 overall best weight: 0.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 463 ASN J 454 GLN K 463 ASN L 312 ASN N 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093443 restraints weight = 75924.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092326 restraints weight = 77311.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093401 restraints weight = 81320.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093558 restraints weight = 53392.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094362 restraints weight = 49001.441| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27517 Z= 0.111 Angle : 0.601 7.936 37317 Z= 0.319 Chirality : 0.044 0.189 4221 Planarity : 0.004 0.042 4858 Dihedral : 5.826 23.470 3696 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.94 (0.13), residues: 3423 helix: -1.67 (0.23), residues: 413 sheet: -0.58 (0.16), residues: 938 loop : -2.84 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 232 TYR 0.016 0.001 TYR I 625 PHE 0.012 0.001 PHE N 455 TRP 0.005 0.001 TRP I 503 HIS 0.002 0.001 HIS L 314 Details of bonding type rmsd covalent geometry : bond 0.00231 (27517) covalent geometry : angle 0.60078 (37317) hydrogen bonds : bond 0.03275 ( 843) hydrogen bonds : angle 5.62218 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 709 TYR cc_start: 0.8352 (m-80) cc_final: 0.7924 (m-10) REVERT: H 710 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6548 (tp30) REVERT: I 710 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6933 (tp30) REVERT: J 380 SER cc_start: 0.8579 (t) cc_final: 0.8298 (m) REVERT: J 452 MET cc_start: 0.6523 (ptt) cc_final: 0.6112 (ptt) REVERT: J 660 MET cc_start: 0.6699 (mpp) cc_final: 0.6419 (mpp) REVERT: K 636 ASN cc_start: 0.6687 (p0) cc_final: 0.4912 (t0) REVERT: K 660 MET cc_start: 0.6266 (mpp) cc_final: 0.5868 (mpp) REVERT: K 736 LEU cc_start: 0.8309 (mp) cc_final: 0.7998 (mp) REVERT: L 710 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7261 (tp30) REVERT: M 382 ASN cc_start: 0.6997 (t0) cc_final: 0.6721 (t0) REVERT: M 709 TYR cc_start: 0.8676 (m-80) cc_final: 0.8382 (m-10) REVERT: N 403 MET cc_start: 0.8702 (tpp) cc_final: 0.8152 (ttm) REVERT: N 710 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6973 (tp30) outliers start: 3 outliers final: 0 residues processed: 270 average time/residue: 0.1688 time to fit residues: 74.0131 Evaluate side-chains 172 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 454 GLN K 610 ASN M 610 ASN N 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.113534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092532 restraints weight = 76079.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091765 restraints weight = 68334.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092513 restraints weight = 76283.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092968 restraints weight = 49542.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093761 restraints weight = 43988.059| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27517 Z= 0.113 Angle : 0.580 8.005 37317 Z= 0.307 Chirality : 0.043 0.176 4221 Planarity : 0.003 0.040 4858 Dihedral : 5.384 21.298 3696 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.68 (0.13), residues: 3423 helix: -1.21 (0.24), residues: 399 sheet: -0.36 (0.16), residues: 952 loop : -2.76 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 668 TYR 0.012 0.001 TYR I 271 PHE 0.015 0.001 PHE K 619 TRP 0.006 0.001 TRP L 632 HIS 0.004 0.002 HIS K 314 Details of bonding type rmsd covalent geometry : bond 0.00239 (27517) covalent geometry : angle 0.57958 (37317) hydrogen bonds : bond 0.03087 ( 843) hydrogen bonds : angle 5.38099 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 709 TYR cc_start: 0.8517 (m-80) cc_final: 0.7971 (m-10) REVERT: H 710 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6536 (tp30) REVERT: I 710 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6641 (tp30) REVERT: J 660 MET cc_start: 0.6708 (mpp) cc_final: 0.6400 (mpp) REVERT: K 620 THR cc_start: 0.6681 (p) cc_final: 0.6367 (p) REVERT: K 636 ASN cc_start: 0.6873 (p0) cc_final: 0.5250 (t0) REVERT: K 660 MET cc_start: 0.6130 (mpp) cc_final: 0.5755 (mpp) REVERT: K 736 LEU cc_start: 0.8330 (mp) cc_final: 0.8007 (mp) REVERT: L 453 ASP cc_start: 0.8296 (t0) cc_final: 0.7993 (t0) REVERT: L 620 THR cc_start: 0.7001 (p) cc_final: 0.6705 (p) REVERT: M 709 TYR cc_start: 0.8728 (m-80) cc_final: 0.8391 (m-10) REVERT: N 403 MET cc_start: 0.8704 (tpp) cc_final: 0.7931 (ttm) REVERT: N 620 THR cc_start: 0.7231 (p) cc_final: 0.7018 (p) REVERT: N 710 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6782 (tp30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1544 time to fit residues: 60.1448 Evaluate side-chains 152 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 195 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 36 optimal weight: 5.9990 chunk 178 optimal weight: 0.0010 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 509 GLN K 610 ASN ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092809 restraints weight = 76407.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091995 restraints weight = 77526.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092812 restraints weight = 83577.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093077 restraints weight = 52238.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093771 restraints weight = 47647.403| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27517 Z= 0.113 Angle : 0.567 7.569 37317 Z= 0.300 Chirality : 0.043 0.193 4221 Planarity : 0.003 0.033 4858 Dihedral : 5.209 20.698 3696 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.53 (0.13), residues: 3423 helix: -1.05 (0.24), residues: 399 sheet: -0.23 (0.16), residues: 966 loop : -2.70 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 668 TYR 0.017 0.001 TYR J 625 PHE 0.008 0.001 PHE M 711 TRP 0.006 0.001 TRP K 632 HIS 0.006 0.004 HIS J 314 Details of bonding type rmsd covalent geometry : bond 0.00251 (27517) covalent geometry : angle 0.56734 (37317) hydrogen bonds : bond 0.03067 ( 843) hydrogen bonds : angle 5.22582 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.7812 (mp10) cc_final: 0.7114 (mp10) REVERT: H 709 TYR cc_start: 0.8470 (m-80) cc_final: 0.7923 (m-10) REVERT: H 710 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6519 (tp30) REVERT: K 432 ASN cc_start: 0.9313 (m-40) cc_final: 0.9077 (m-40) REVERT: K 636 ASN cc_start: 0.6361 (p0) cc_final: 0.4782 (t0) REVERT: K 660 MET cc_start: 0.6186 (mpp) cc_final: 0.5843 (mpp) REVERT: L 620 THR cc_start: 0.7047 (p) cc_final: 0.6798 (p) REVERT: M 660 MET cc_start: 0.6620 (mpp) cc_final: 0.6396 (mpp) REVERT: M 709 TYR cc_start: 0.8812 (m-80) cc_final: 0.8557 (m-10) REVERT: N 403 MET cc_start: 0.8674 (tpp) cc_final: 0.7860 (ttm) REVERT: N 710 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6951 (tp30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1555 time to fit residues: 59.5631 Evaluate side-chains 153 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 164 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 207 optimal weight: 0.0670 chunk 280 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 297 optimal weight: 0.2980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 312 ASN ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.111173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090485 restraints weight = 76325.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089100 restraints weight = 72969.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089921 restraints weight = 72591.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.090795 restraints weight = 49485.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.091023 restraints weight = 43249.515| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27517 Z= 0.144 Angle : 0.595 7.466 37317 Z= 0.316 Chirality : 0.044 0.234 4221 Planarity : 0.003 0.040 4858 Dihedral : 5.269 22.198 3696 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.48 (0.14), residues: 3423 helix: -0.97 (0.24), residues: 392 sheet: -0.21 (0.16), residues: 966 loop : -2.66 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 668 TYR 0.018 0.001 TYR N 271 PHE 0.017 0.002 PHE H 711 TRP 0.008 0.001 TRP M 503 HIS 0.009 0.005 HIS L 314 Details of bonding type rmsd covalent geometry : bond 0.00323 (27517) covalent geometry : angle 0.59462 (37317) hydrogen bonds : bond 0.03382 ( 843) hydrogen bonds : angle 5.16172 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.8055 (mp10) cc_final: 0.7261 (mp10) REVERT: I 709 TYR cc_start: 0.8632 (m-80) cc_final: 0.8371 (m-10) REVERT: J 709 TYR cc_start: 0.8674 (m-80) cc_final: 0.8285 (m-10) REVERT: K 432 ASN cc_start: 0.9305 (m-40) cc_final: 0.9081 (m-40) REVERT: K 609 MET cc_start: 0.7225 (mtt) cc_final: 0.6951 (ttm) REVERT: K 660 MET cc_start: 0.6596 (mpp) cc_final: 0.6062 (mpp) REVERT: L 453 ASP cc_start: 0.8254 (t0) cc_final: 0.7937 (t0) REVERT: L 466 GLN cc_start: 0.8047 (mp10) cc_final: 0.7660 (mp10) REVERT: L 620 THR cc_start: 0.7148 (p) cc_final: 0.6883 (p) REVERT: L 660 MET cc_start: 0.6963 (mpp) cc_final: 0.6615 (mpp) REVERT: L 709 TYR cc_start: 0.8152 (m-10) cc_final: 0.7935 (m-10) REVERT: N 403 MET cc_start: 0.8543 (tpp) cc_final: 0.8071 (ttm) REVERT: N 710 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6801 (tp30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1685 time to fit residues: 58.4149 Evaluate side-chains 137 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088343 restraints weight = 76888.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087088 restraints weight = 74810.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087765 restraints weight = 76446.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088504 restraints weight = 50384.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088721 restraints weight = 43771.162| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27517 Z= 0.206 Angle : 0.655 7.145 37317 Z= 0.349 Chirality : 0.046 0.224 4221 Planarity : 0.004 0.090 4858 Dihedral : 5.651 23.115 3696 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.52 (0.14), residues: 3423 helix: -1.18 (0.23), residues: 399 sheet: -0.37 (0.16), residues: 1015 loop : -2.63 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 232 TYR 0.022 0.002 TYR K 271 PHE 0.017 0.002 PHE M 487 TRP 0.009 0.001 TRP K 245 HIS 0.012 0.006 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00465 (27517) covalent geometry : angle 0.65514 (37317) hydrogen bonds : bond 0.03804 ( 843) hydrogen bonds : angle 5.25859 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.8305 (mp10) cc_final: 0.7301 (mp10) REVERT: J 660 MET cc_start: 0.6695 (mpp) cc_final: 0.6365 (mpp) REVERT: J 709 TYR cc_start: 0.8692 (m-80) cc_final: 0.8308 (m-10) REVERT: K 432 ASN cc_start: 0.9381 (m-40) cc_final: 0.9148 (m-40) REVERT: K 463 ASN cc_start: 0.8003 (t0) cc_final: 0.7762 (t0) REVERT: K 609 MET cc_start: 0.7587 (mtt) cc_final: 0.7384 (ttm) REVERT: K 660 MET cc_start: 0.6554 (mpp) cc_final: 0.5992 (mpp) REVERT: K 668 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7547 (ptp-170) REVERT: L 466 GLN cc_start: 0.8141 (mp10) cc_final: 0.7636 (mp10) REVERT: L 620 THR cc_start: 0.7136 (p) cc_final: 0.6878 (p) REVERT: L 709 TYR cc_start: 0.8239 (m-10) cc_final: 0.7951 (m-10) REVERT: M 382 ASN cc_start: 0.6963 (t0) cc_final: 0.6701 (p0) REVERT: N 403 MET cc_start: 0.8575 (tpp) cc_final: 0.7852 (ttm) REVERT: N 432 ASN cc_start: 0.9306 (m-40) cc_final: 0.9101 (m-40) REVERT: N 453 ASP cc_start: 0.8525 (t0) cc_final: 0.8269 (t0) REVERT: N 697 TYR cc_start: 0.5425 (t80) cc_final: 0.4987 (t80) REVERT: N 710 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6657 (tp30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1633 time to fit residues: 51.5678 Evaluate side-chains 132 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 65 optimal weight: 6.9990 chunk 177 optimal weight: 0.4980 chunk 321 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 ASN ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 ASN ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 ASN ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087523 restraints weight = 77321.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088220 restraints weight = 76151.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088251 restraints weight = 71675.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088435 restraints weight = 46067.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088622 restraints weight = 41304.241| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27517 Z= 0.227 Angle : 0.686 7.688 37317 Z= 0.368 Chirality : 0.046 0.192 4221 Planarity : 0.004 0.071 4858 Dihedral : 5.999 23.691 3696 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.10 % Allowed : 1.40 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.61 (0.14), residues: 3423 helix: -1.41 (0.22), residues: 399 sheet: -0.50 (0.16), residues: 1015 loop : -2.60 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 232 TYR 0.022 0.002 TYR K 271 PHE 0.020 0.002 PHE M 487 TRP 0.010 0.001 TRP N 245 HIS 0.011 0.007 HIS N 314 Details of bonding type rmsd covalent geometry : bond 0.00512 (27517) covalent geometry : angle 0.68617 (37317) hydrogen bonds : bond 0.04024 ( 843) hydrogen bonds : angle 5.42037 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.8323 (mp10) cc_final: 0.7314 (mp10) REVERT: I 453 ASP cc_start: 0.8370 (t0) cc_final: 0.7887 (t0) REVERT: J 709 TYR cc_start: 0.8757 (m-80) cc_final: 0.8313 (m-10) REVERT: K 432 ASN cc_start: 0.9398 (m-40) cc_final: 0.9166 (m-40) REVERT: K 553 LYS cc_start: 0.8283 (tttt) cc_final: 0.7974 (mttt) REVERT: K 660 MET cc_start: 0.6472 (mpp) cc_final: 0.5943 (mpp) REVERT: L 466 GLN cc_start: 0.7888 (mp10) cc_final: 0.7622 (mp10) REVERT: L 620 THR cc_start: 0.7486 (p) cc_final: 0.7231 (p) REVERT: M 609 MET cc_start: 0.7869 (ttm) cc_final: 0.7635 (ttm) REVERT: N 403 MET cc_start: 0.8509 (tpp) cc_final: 0.8140 (ttm) REVERT: N 453 ASP cc_start: 0.8392 (t0) cc_final: 0.8124 (t0) REVERT: N 697 TYR cc_start: 0.5711 (t80) cc_final: 0.5353 (t80) outliers start: 3 outliers final: 0 residues processed: 181 average time/residue: 0.1553 time to fit residues: 46.5827 Evaluate side-chains 129 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 15 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 332 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 ASN ** J 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 ASN ** K 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 ASN L 454 GLN ** M 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.109909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089220 restraints weight = 76923.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087886 restraints weight = 74104.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088630 restraints weight = 75825.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089534 restraints weight = 51311.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089721 restraints weight = 44391.281| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27517 Z= 0.147 Angle : 0.617 6.089 37317 Z= 0.328 Chirality : 0.045 0.195 4221 Planarity : 0.004 0.062 4858 Dihedral : 5.688 23.104 3696 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.10 % Allowed : 0.82 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.50 (0.14), residues: 3423 helix: -1.29 (0.23), residues: 399 sheet: -0.40 (0.16), residues: 1015 loop : -2.55 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 528 TYR 0.016 0.001 TYR N 601 PHE 0.013 0.002 PHE M 487 TRP 0.006 0.001 TRP L 632 HIS 0.006 0.003 HIS M 314 Details of bonding type rmsd covalent geometry : bond 0.00329 (27517) covalent geometry : angle 0.61713 (37317) hydrogen bonds : bond 0.03492 ( 843) hydrogen bonds : angle 5.20267 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 466 GLN cc_start: 0.8294 (mp10) cc_final: 0.7228 (mp10) REVERT: I 453 ASP cc_start: 0.8408 (t0) cc_final: 0.7981 (t0) REVERT: I 660 MET cc_start: 0.6347 (mpp) cc_final: 0.6127 (mpp) REVERT: J 660 MET cc_start: 0.6581 (mpp) cc_final: 0.6345 (mpp) REVERT: J 709 TYR cc_start: 0.8680 (m-80) cc_final: 0.8172 (m-10) REVERT: K 432 ASN cc_start: 0.9373 (m-40) cc_final: 0.9146 (m-40) REVERT: K 463 ASN cc_start: 0.8436 (t0) cc_final: 0.8197 (t0) REVERT: K 609 MET cc_start: 0.7292 (ttm) cc_final: 0.6786 (ttm) REVERT: K 660 MET cc_start: 0.6461 (mpp) cc_final: 0.5937 (mpp) REVERT: L 620 THR cc_start: 0.7573 (p) cc_final: 0.7330 (p) REVERT: M 609 MET cc_start: 0.7674 (ttm) cc_final: 0.7202 (ttm) REVERT: N 403 MET cc_start: 0.8407 (tpp) cc_final: 0.8076 (ttm) REVERT: N 453 ASP cc_start: 0.8396 (t0) cc_final: 0.8116 (t0) outliers start: 3 outliers final: 0 residues processed: 180 average time/residue: 0.1558 time to fit residues: 46.5281 Evaluate side-chains 129 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 124 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 302 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 ASN I 382 ASN J 382 ASN K 382 ASN K 509 GLN ** M 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 382 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.111368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091074 restraints weight = 76802.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090415 restraints weight = 74130.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091052 restraints weight = 83122.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091556 restraints weight = 50810.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092083 restraints weight = 45360.836| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27517 Z= 0.118 Angle : 0.601 8.047 37317 Z= 0.316 Chirality : 0.044 0.206 4221 Planarity : 0.003 0.054 4858 Dihedral : 5.389 23.856 3696 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.16 % Allowed : 0.23 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.39 (0.14), residues: 3423 helix: -1.03 (0.24), residues: 392 sheet: -0.24 (0.16), residues: 966 loop : -2.51 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 668 TYR 0.015 0.001 TYR M 625 PHE 0.010 0.001 PHE I 619 TRP 0.006 0.001 TRP L 375 HIS 0.004 0.002 HIS I 314 Details of bonding type rmsd covalent geometry : bond 0.00262 (27517) covalent geometry : angle 0.60069 (37317) hydrogen bonds : bond 0.03152 ( 843) hydrogen bonds : angle 5.06515 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 304 MET cc_start: 0.8518 (tpp) cc_final: 0.7845 (tpp) REVERT: H 466 GLN cc_start: 0.8121 (mp10) cc_final: 0.7125 (mp10) REVERT: H 709 TYR cc_start: 0.8456 (m-80) cc_final: 0.8082 (m-10) REVERT: I 453 ASP cc_start: 0.8373 (t0) cc_final: 0.7952 (t0) REVERT: J 463 ASN cc_start: 0.7346 (t0) cc_final: 0.7083 (t0) REVERT: J 709 TYR cc_start: 0.8603 (m-80) cc_final: 0.8265 (m-10) REVERT: K 432 ASN cc_start: 0.9358 (m-40) cc_final: 0.9136 (m-40) REVERT: K 609 MET cc_start: 0.7130 (ttm) cc_final: 0.6697 (ttm) REVERT: K 660 MET cc_start: 0.6460 (mpp) cc_final: 0.5945 (mpp) REVERT: L 620 THR cc_start: 0.7482 (p) cc_final: 0.7218 (p) REVERT: L 660 MET cc_start: 0.6908 (mpp) cc_final: 0.6687 (mpp) REVERT: M 609 MET cc_start: 0.7686 (ttm) cc_final: 0.7042 (ttm) REVERT: N 403 MET cc_start: 0.8440 (tpp) cc_final: 0.8232 (ttm) REVERT: N 453 ASP cc_start: 0.8438 (t0) cc_final: 0.8183 (t0) REVERT: N 697 TYR cc_start: 0.5724 (t80) cc_final: 0.5409 (t80) outliers start: 5 outliers final: 0 residues processed: 182 average time/residue: 0.1570 time to fit residues: 47.6763 Evaluate side-chains 128 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 chunk 238 optimal weight: 0.0570 chunk 110 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 382 ASN ** I 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 ASN K 382 ASN ** L 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089936 restraints weight = 76410.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088881 restraints weight = 69931.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089673 restraints weight = 78124.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089947 restraints weight = 51982.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090616 restraints weight = 46075.869| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27517 Z= 0.142 Angle : 0.613 6.259 37317 Z= 0.323 Chirality : 0.044 0.251 4221 Planarity : 0.004 0.054 4858 Dihedral : 5.375 24.047 3696 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.10 % Allowed : 0.23 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -2.34 (0.14), residues: 3423 helix: -0.99 (0.24), residues: 392 sheet: -0.21 (0.16), residues: 966 loop : -2.49 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 668 TYR 0.017 0.001 TYR K 625 PHE 0.019 0.002 PHE L 555 TRP 0.006 0.001 TRP N 245 HIS 0.009 0.005 HIS L 314 Details of bonding type rmsd covalent geometry : bond 0.00321 (27517) covalent geometry : angle 0.61264 (37317) hydrogen bonds : bond 0.03324 ( 843) hydrogen bonds : angle 5.06457 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.33 seconds wall clock time: 53 minutes 49.23 seconds (3229.23 seconds total)