Starting phenix.real_space_refine on Thu Sep 18 20:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7k_44314/09_2025/9b7k_44314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7k_44314/09_2025/9b7k_44314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b7k_44314/09_2025/9b7k_44314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7k_44314/09_2025/9b7k_44314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7k_44314/09_2025/9b7k_44314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7k_44314/09_2025/9b7k_44314.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 12964 2.51 5 N 3579 2.21 5 O 3944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20567 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3694 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 433} Chain breaks: 1 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 196} Chain breaks: 1 Chain: "C" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4047 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 473} Chain breaks: 1 Chain: "D" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3702 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 434} Chain breaks: 1 Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 196} Chain breaks: 1 Chain: "F" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3962 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1009 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.67, per 1000 atoms: 0.23 Number of scatterers: 20567 At special positions: 0 Unit cell: (170.2, 136.9, 100.825, 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 80 16.00 O 3944 8.00 N 3579 7.00 C 12964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 577.6 milliseconds Enol-peptide restraints added in 12.4 microseconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 55 sheets defined 8.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.964A pdb=" N ASN A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.524A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 569 removed outlier: 4.228A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 564 through 569 removed outlier: 3.969A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.874A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.611A pdb=" N PHE C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 564 through 569 removed outlier: 4.335A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 removed outlier: 4.092A pdb=" N HIS D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.849A pdb=" N ASN D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.654A pdb=" N PHE D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 removed outlier: 4.050A pdb=" N LEU D 435 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 564 through 569 removed outlier: 4.115A pdb=" N THR D 568 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'E' and resid 564 through 569 removed outlier: 4.062A pdb=" N THR E 568 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.253A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.857A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.810A pdb=" N PHE F 400 " --> pdb=" O LEU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 435 removed outlier: 4.079A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 563 through 569 removed outlier: 4.401A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.595A pdb=" N ASN H 50 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.676A pdb=" N TYR H 134 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 238 through 249 current: chain 'A' and resid 331 through 336 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.337A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.107A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA9, first strand: chain 'A' and resid 593 through 596 removed outlier: 4.097A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 619 through 621 Processing sheet with id=AB2, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.409A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 449 removed outlier: 5.697A pdb=" N LEU B 447 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER B 464 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.596A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.999A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 619 through 621 Processing sheet with id=AB9, first strand: chain 'C' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 238 through 250 current: chain 'C' and resid 331 through 336 Processing sheet with id=AC1, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AC2, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.386A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 445 through 451 removed outlier: 7.028A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC7, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AC8, first strand: chain 'D' and resid 232 through 235 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 238 through 249 current: chain 'D' and resid 333 through 336 Processing sheet with id=AC9, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AD1, first strand: chain 'D' and resid 445 through 451 removed outlier: 6.805A pdb=" N LYS D 462 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 450 " --> pdb=" O THR D 460 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.358A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD5, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.110A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD7, first strand: chain 'D' and resid 593 through 596 removed outlier: 4.113A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 619 through 621 Processing sheet with id=AD9, first strand: chain 'D' and resid 627 through 628 removed outlier: 6.463A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 445 through 451 removed outlier: 6.888A pdb=" N LYS E 462 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR E 450 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.149A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 483 through 484 removed outlier: 3.522A pdb=" N SER E 483 " --> pdb=" O GLN E 599 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE5, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.107A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 619 through 621 removed outlier: 5.940A pdb=" N ALA E 620 " --> pdb=" O MET E 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 232 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 331 through 336 Processing sheet with id=AE8, first strand: chain 'F' and resid 258 through 261 removed outlier: 7.509A pdb=" N THR F 279 " --> pdb=" O TYR F 379 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR F 379 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP F 281 " --> pdb=" O TYR F 377 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 342 through 344 Processing sheet with id=AF1, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.448A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 445 through 451 removed outlier: 6.798A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AF4, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AF5, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AF6, first strand: chain 'F' and resid 619 through 621 removed outlier: 6.095A pdb=" N ALA F 620 " --> pdb=" O MET F 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AF8, first strand: chain 'H' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 30 through 31 current: chain 'H' and resid 64 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 136 through 138 Processing sheet with id=AF9, first strand: chain 'L' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 32 current: chain 'L' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 69 current: chain 'L' and resid 119 through 122 No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 38 through 43 276 hydrogen bonds defined for protein. 564 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: 3.34 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3626 1.32 - 1.44: 6171 1.44 - 1.57: 11236 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 21173 Sorted by residual: bond pdb=" C ASN H 78 " pdb=" O ASN H 78 " ideal model delta sigma weight residual 1.234 1.198 0.036 1.26e-02 6.30e+03 8.20e+00 bond pdb=" C PRO F 365 " pdb=" O PRO F 365 " ideal model delta sigma weight residual 1.246 1.224 0.021 8.50e-03 1.38e+04 6.33e+00 bond pdb=" C PRO D 365 " pdb=" O PRO D 365 " ideal model delta sigma weight residual 1.243 1.223 0.021 8.50e-03 1.38e+04 5.89e+00 bond pdb=" C ILE C 240 " pdb=" O ILE C 240 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.09e-02 8.42e+03 4.35e+00 bond pdb=" C ILE H 70 " pdb=" O ILE H 70 " ideal model delta sigma weight residual 1.235 1.215 0.021 9.90e-03 1.02e+04 4.30e+00 ... (remaining 21168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 28041 2.53 - 5.06: 697 5.06 - 7.59: 68 7.59 - 10.13: 17 10.13 - 12.66: 5 Bond angle restraints: 28828 Sorted by residual: angle pdb=" N GLY C 539 " pdb=" CA GLY C 539 " pdb=" C GLY C 539 " ideal model delta sigma weight residual 112.73 122.53 -9.80 1.20e+00 6.94e-01 6.67e+01 angle pdb=" N SER F 448 " pdb=" CA SER F 448 " pdb=" C SER F 448 " ideal model delta sigma weight residual 111.36 118.92 -7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N TYR F 706 " pdb=" CA TYR F 706 " pdb=" C TYR F 706 " ideal model delta sigma weight residual 110.53 119.24 -8.71 1.32e+00 5.74e-01 4.36e+01 angle pdb=" N ASP C 551 " pdb=" CA ASP C 551 " pdb=" C ASP C 551 " ideal model delta sigma weight residual 108.90 119.65 -10.75 1.63e+00 3.76e-01 4.35e+01 angle pdb=" C GLU F 723 " pdb=" N PRO F 724 " pdb=" CA PRO F 724 " ideal model delta sigma weight residual 118.85 125.89 -7.04 1.09e+00 8.42e-01 4.17e+01 ... (remaining 28823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11753 17.92 - 35.84: 476 35.84 - 53.76: 81 53.76 - 71.68: 26 71.68 - 89.60: 14 Dihedral angle restraints: 12350 sinusoidal: 4881 harmonic: 7469 Sorted by residual: dihedral pdb=" CA ASN A 519 " pdb=" C ASN A 519 " pdb=" N PRO A 520 " pdb=" CA PRO A 520 " ideal model delta harmonic sigma weight residual 0.00 -31.09 31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ASN B 519 " pdb=" C ASN B 519 " pdb=" N PRO B 520 " pdb=" CA PRO B 520 " ideal model delta harmonic sigma weight residual 0.00 -28.00 28.00 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASN E 519 " pdb=" C ASN E 519 " pdb=" N PRO E 520 " pdb=" CA PRO E 520 " ideal model delta harmonic sigma weight residual 0.00 -26.51 26.51 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 12347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2613 0.101 - 0.202: 295 0.202 - 0.303: 35 0.303 - 0.403: 4 0.403 - 0.504: 4 Chirality restraints: 2951 Sorted by residual: chirality pdb=" CA HIS A 290 " pdb=" N HIS A 290 " pdb=" C HIS A 290 " pdb=" CB HIS A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CA HIS C 290 " pdb=" N HIS C 290 " pdb=" C HIS C 290 " pdb=" CB HIS C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CA SER L 117 " pdb=" N SER L 117 " pdb=" C SER L 117 " pdb=" CB SER L 117 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 2948 not shown) Planarity restraints: 3837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 108 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C GLU H 108 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU H 108 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP H 109 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 67 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C VAL H 67 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL H 67 " 0.015 2.00e-02 2.50e+03 pdb=" N SER H 68 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 422 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C PHE F 422 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE F 422 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS F 423 " -0.013 2.00e-02 2.50e+03 ... (remaining 3834 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 167 2.54 - 3.13: 15998 3.13 - 3.72: 32178 3.72 - 4.31: 48689 4.31 - 4.90: 80087 Nonbonded interactions: 177119 Sorted by model distance: nonbonded pdb=" OE1 GLU C 529 " pdb=" NZ LYS C 567 " model vdw 1.956 3.120 nonbonded pdb=" OE2 GLU C 563 " pdb=" OH TYR C 613 " model vdw 2.004 3.040 nonbonded pdb=" CD ARG D 238 " pdb=" OE2 GLU D 684 " model vdw 2.042 3.440 nonbonded pdb=" OH TYR C 415 " pdb=" O HIS C 642 " model vdw 2.064 3.040 nonbonded pdb=" OH TYR A 252 " pdb=" O ILE A 374 " model vdw 2.090 3.040 ... (remaining 177114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 220 through 644 or resid 649 through 650 or resid 668 or r \ esid 676 or resid 679 or resid 682 through 683 or resid 687)) selection = (chain 'C' and (resid 220 through 438 or resid 442 through 644 or resid 649 thro \ ugh 650 or resid 668 or resid 676 or resid 679 or resid 682 through 683 or resid \ 687)) selection = (chain 'D' and (resid 220 through 644 or resid 649 through 650 or resid 668 or r \ esid 676 or resid 679 or resid 682 through 683 or resid 687)) selection = (chain 'F' and (resid 220 through 438 or resid 442 through 644 or resid 671 or r \ esid 689 or resid 709 or resid 717 or resid 720 or resid 723 or resid 727 or res \ id 732)) } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.760 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21175 Z= 0.330 Angle : 0.928 12.657 28832 Z= 0.591 Chirality : 0.068 0.504 2951 Planarity : 0.005 0.042 3837 Dihedral : 10.923 89.601 7592 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.32 % Allowed : 2.99 % Favored : 94.69 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.14), residues: 2577 helix: -3.77 (0.26), residues: 100 sheet: -0.21 (0.17), residues: 733 loop : -0.58 (0.12), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 730 TYR 0.024 0.002 TYR F 705 PHE 0.021 0.002 PHE C 367 TRP 0.027 0.002 TRP F 228 HIS 0.012 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00548 (21173) covalent geometry : angle 0.92776 (28828) SS BOND : bond 0.00360 ( 2) SS BOND : angle 0.27376 ( 4) hydrogen bonds : bond 0.24793 ( 276) hydrogen bonds : angle 8.63853 ( 564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 400 time to evaluate : 0.683 Fit side-chains REVERT: A 300 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7830 (ttp-110) REVERT: A 333 THR cc_start: 0.7525 (m) cc_final: 0.7308 (p) REVERT: A 337 ASN cc_start: 0.7657 (t0) cc_final: 0.7247 (t0) REVERT: A 449 LYS cc_start: 0.7960 (mttt) cc_final: 0.7449 (mttt) REVERT: A 546 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7543 (mt0) REVERT: B 514 ARG cc_start: 0.8095 (mtm180) cc_final: 0.6305 (mtp180) REVERT: C 488 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8475 (ttp-170) REVERT: C 668 ASN cc_start: 0.7367 (p0) cc_final: 0.7067 (m-40) REVERT: D 235 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7555 (pt) REVERT: D 297 ASP cc_start: 0.7683 (m-30) cc_final: 0.7473 (m-30) REVERT: F 258 LYS cc_start: 0.8453 (mtmt) cc_final: 0.7757 (tptt) REVERT: F 387 GLN cc_start: 0.8041 (mt0) cc_final: 0.7807 (mt0) REVERT: L 63 THR cc_start: 0.8199 (m) cc_final: 0.7933 (t) outliers start: 52 outliers final: 26 residues processed: 440 average time/residue: 0.6022 time to fit residues: 298.1835 Evaluate side-chains 268 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 259 GLN A 262 ASN A 290 HIS A 437 ASN A 570 ASN A 588 GLN A 590 GLN A 608 GLN A 624 HIS A 646 GLN A 651 ASN A 678 GLN B 428 HIS B 430 GLN B 458 GLN B 615 GLN B 624 HIS C 319 ASN C 321 GLN C 452 ASN C 497 ASN C 515 ASN C 608 GLN C 646 GLN C 651 ASN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN D 229 HIS D 262 ASN D 343 GLN D 376 GLN D 497 ASN D 546 GLN D 585 GLN D 608 GLN D 624 HIS D 646 GLN D 673 GLN E 452 ASN E 496 ASN E 608 GLN E 624 HIS F 255 HIS ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN F 412 GLN F 430 GLN F 452 ASN F 470 ASN F 546 GLN F 608 GLN F 673 GLN F 700 GLN H 22 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.096889 restraints weight = 29087.767| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.71 r_work: 0.2948 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21175 Z= 0.273 Angle : 0.663 10.757 28832 Z= 0.352 Chirality : 0.049 0.163 2951 Planarity : 0.005 0.054 3837 Dihedral : 6.844 58.658 2870 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.06 % Allowed : 8.38 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 2577 helix: -3.27 (0.37), residues: 107 sheet: -0.24 (0.18), residues: 641 loop : -0.55 (0.12), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 391 TYR 0.021 0.002 TYR L 57 PHE 0.018 0.002 PHE C 367 TRP 0.019 0.002 TRP F 228 HIS 0.019 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00649 (21173) covalent geometry : angle 0.66282 (28828) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.70929 ( 4) hydrogen bonds : bond 0.04203 ( 276) hydrogen bonds : angle 6.53175 ( 564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 241 time to evaluate : 0.801 Fit side-chains REVERT: A 300 ARG cc_start: 0.7615 (ttm110) cc_final: 0.7216 (ttp-110) REVERT: A 333 THR cc_start: 0.7580 (m) cc_final: 0.7133 (p) REVERT: A 398 GLU cc_start: 0.8353 (mp0) cc_final: 0.8016 (mp0) REVERT: A 449 LYS cc_start: 0.7931 (mttt) cc_final: 0.7062 (mttt) REVERT: A 546 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7478 (mt0) REVERT: A 682 GLU cc_start: 0.7865 (tt0) cc_final: 0.7263 (tm-30) REVERT: B 441 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: B 514 ARG cc_start: 0.8021 (mtm180) cc_final: 0.5704 (mtp180) REVERT: C 554 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: C 668 ASN cc_start: 0.7581 (p0) cc_final: 0.7146 (m-40) REVERT: D 238 ARG cc_start: 0.7080 (tpt170) cc_final: 0.6784 (mmt-90) REVERT: D 297 ASP cc_start: 0.7249 (m-30) cc_final: 0.6976 (m-30) REVERT: D 686 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: E 641 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7603 (mtpt) REVERT: F 258 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7185 (tptt) REVERT: F 387 GLN cc_start: 0.8168 (mt0) cc_final: 0.7798 (mt0) REVERT: F 398 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.3913 (tm-30) REVERT: H 108 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7898 (mp0) outliers start: 91 outliers final: 44 residues processed: 299 average time/residue: 0.6247 time to fit residues: 210.3465 Evaluate side-chains 265 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 419 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 734 ARG Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 141 GLN Chi-restraints excluded: chain H residue 143 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 52 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 173 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 337 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 673 GLN D 262 ASN D 546 GLN D 585 GLN E 496 ASN F 229 HIS ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 403 GLN F 412 GLN H 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099109 restraints weight = 29045.229| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.73 r_work: 0.2967 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21175 Z= 0.124 Angle : 0.522 11.529 28832 Z= 0.272 Chirality : 0.042 0.150 2951 Planarity : 0.004 0.040 3837 Dihedral : 5.752 58.842 2848 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.76 % Allowed : 10.25 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 2577 helix: -2.57 (0.44), residues: 101 sheet: -0.10 (0.19), residues: 644 loop : -0.41 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 238 TYR 0.011 0.001 TYR C 706 PHE 0.012 0.001 PHE E 535 TRP 0.015 0.001 TRP H 66 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00288 (21173) covalent geometry : angle 0.52222 (28828) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.67521 ( 4) hydrogen bonds : bond 0.02930 ( 276) hydrogen bonds : angle 5.87651 ( 564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 0.760 Fit side-chains REVERT: A 300 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7208 (ttp-110) REVERT: A 333 THR cc_start: 0.7663 (m) cc_final: 0.7343 (p) REVERT: A 398 GLU cc_start: 0.8356 (mp0) cc_final: 0.7986 (mp0) REVERT: A 449 LYS cc_start: 0.7926 (mttt) cc_final: 0.7072 (mttt) REVERT: A 546 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7505 (mt0) REVERT: A 682 GLU cc_start: 0.7897 (tt0) cc_final: 0.7236 (tm-30) REVERT: B 441 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: B 456 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8071 (mm110) REVERT: B 514 ARG cc_start: 0.7996 (mtm180) cc_final: 0.5746 (mtp180) REVERT: C 605 MET cc_start: 0.9137 (mtt) cc_final: 0.8851 (ttt) REVERT: C 668 ASN cc_start: 0.7484 (p0) cc_final: 0.7155 (m-40) REVERT: D 238 ARG cc_start: 0.6927 (tpt170) cc_final: 0.6506 (tpt170) REVERT: D 297 ASP cc_start: 0.7342 (m-30) cc_final: 0.7085 (m-30) REVERT: D 686 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: E 641 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7658 (mttt) REVERT: F 258 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7177 (tptt) REVERT: F 387 GLN cc_start: 0.8187 (mt0) cc_final: 0.7820 (mt0) REVERT: F 445 TYR cc_start: 0.8141 (m-80) cc_final: 0.7936 (m-80) REVERT: F 641 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8604 (mttm) REVERT: H 101 GLU cc_start: 0.8656 (tt0) cc_final: 0.8305 (tt0) REVERT: H 108 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: L 63 THR cc_start: 0.8306 (m) cc_final: 0.7837 (t) outliers start: 62 outliers final: 37 residues processed: 296 average time/residue: 0.5771 time to fit residues: 193.5067 Evaluate side-chains 266 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 565 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 141 GLN Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 174 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 253 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 184 optimal weight: 40.0000 chunk 57 optimal weight: 8.9990 chunk 128 optimal weight: 0.0870 overall best weight: 2.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 337 ASN A 588 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 HIS D 585 GLN E 496 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 403 GLN H 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.097904 restraints weight = 29196.965| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.73 r_work: 0.2967 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21175 Z= 0.152 Angle : 0.522 9.959 28832 Z= 0.271 Chirality : 0.043 0.146 2951 Planarity : 0.004 0.040 3837 Dihedral : 5.485 54.410 2841 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.94 % Allowed : 11.23 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.15), residues: 2577 helix: -2.51 (0.46), residues: 101 sheet: -0.02 (0.19), residues: 649 loop : -0.38 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 238 TYR 0.014 0.001 TYR L 57 PHE 0.013 0.001 PHE E 535 TRP 0.016 0.001 TRP H 66 HIS 0.009 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00362 (21173) covalent geometry : angle 0.52186 (28828) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.59031 ( 4) hydrogen bonds : bond 0.02793 ( 276) hydrogen bonds : angle 5.66378 ( 564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 0.824 Fit side-chains REVERT: A 300 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7177 (ttp-110) REVERT: A 333 THR cc_start: 0.7681 (m) cc_final: 0.7383 (p) REVERT: A 398 GLU cc_start: 0.8380 (mp0) cc_final: 0.7962 (mp0) REVERT: A 449 LYS cc_start: 0.7952 (mttt) cc_final: 0.6990 (mttt) REVERT: A 546 GLN cc_start: 0.8308 (tp-100) cc_final: 0.7499 (mt0) REVERT: A 565 GLU cc_start: 0.8054 (mp0) cc_final: 0.7765 (mp0) REVERT: A 682 GLU cc_start: 0.7918 (tt0) cc_final: 0.7215 (tm-30) REVERT: B 441 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: B 456 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8036 (mm110) REVERT: B 514 ARG cc_start: 0.8026 (mtm180) cc_final: 0.5779 (mtp180) REVERT: C 588 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: C 605 MET cc_start: 0.9176 (mtt) cc_final: 0.8940 (ttt) REVERT: C 668 ASN cc_start: 0.7491 (p0) cc_final: 0.7154 (m-40) REVERT: D 238 ARG cc_start: 0.6994 (tpt170) cc_final: 0.6590 (tpt170) REVERT: D 297 ASP cc_start: 0.7324 (m-30) cc_final: 0.7071 (m-30) REVERT: D 686 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: E 641 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7661 (mttt) REVERT: F 258 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7159 (tptt) REVERT: F 398 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.3695 (tm-30) REVERT: F 403 GLN cc_start: 0.7940 (tt0) cc_final: 0.7478 (tt0) REVERT: F 641 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8612 (mttm) REVERT: H 101 GLU cc_start: 0.8699 (tt0) cc_final: 0.8304 (tt0) REVERT: H 108 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7934 (mp0) outliers start: 66 outliers final: 37 residues processed: 275 average time/residue: 0.6167 time to fit residues: 191.3624 Evaluate side-chains 265 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 419 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 51 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 163 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 chunk 193 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 337 ASN A 588 GLN A 673 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN E 496 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN H 22 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098514 restraints weight = 28868.849| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.73 r_work: 0.2980 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21175 Z= 0.125 Angle : 0.498 11.169 28832 Z= 0.257 Chirality : 0.042 0.147 2951 Planarity : 0.004 0.038 3837 Dihedral : 5.173 49.999 2839 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.63 % Allowed : 12.30 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 2577 helix: -2.48 (0.47), residues: 101 sheet: -0.00 (0.19), residues: 655 loop : -0.34 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 238 TYR 0.011 0.001 TYR L 57 PHE 0.012 0.001 PHE E 535 TRP 0.015 0.001 TRP H 66 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00294 (21173) covalent geometry : angle 0.49759 (28828) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.57474 ( 4) hydrogen bonds : bond 0.02552 ( 276) hydrogen bonds : angle 5.42740 ( 564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 0.739 Fit side-chains REVERT: A 300 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7258 (ttp-110) REVERT: A 333 THR cc_start: 0.7683 (m) cc_final: 0.7446 (p) REVERT: A 398 GLU cc_start: 0.8403 (mp0) cc_final: 0.7991 (mp0) REVERT: A 449 LYS cc_start: 0.7978 (mttt) cc_final: 0.6946 (mttt) REVERT: A 458 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7113 (mm-40) REVERT: A 565 GLU cc_start: 0.8026 (mp0) cc_final: 0.7753 (mp0) REVERT: A 588 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: B 456 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8038 (mm110) REVERT: B 514 ARG cc_start: 0.8054 (mtm180) cc_final: 0.5699 (mtp180) REVERT: B 562 ASN cc_start: 0.8115 (p0) cc_final: 0.7680 (p0) REVERT: C 668 ASN cc_start: 0.7471 (p0) cc_final: 0.7136 (m-40) REVERT: C 712 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 297 ASP cc_start: 0.7324 (m-30) cc_final: 0.7089 (m-30) REVERT: D 686 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: E 418 GLU cc_start: 0.7790 (pt0) cc_final: 0.7577 (pt0) REVERT: E 641 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7681 (mttt) REVERT: F 258 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7152 (tptt) REVERT: F 398 GLU cc_start: 0.4392 (OUTLIER) cc_final: 0.3864 (tm-30) REVERT: F 403 GLN cc_start: 0.7939 (tt0) cc_final: 0.7459 (tt0) REVERT: F 641 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8633 (mttm) REVERT: H 88 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8996 (m) REVERT: H 101 GLU cc_start: 0.8665 (tt0) cc_final: 0.8324 (tt0) REVERT: H 108 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: L 63 THR cc_start: 0.8290 (m) cc_final: 0.7895 (t) outliers start: 59 outliers final: 34 residues processed: 278 average time/residue: 0.5981 time to fit residues: 188.3227 Evaluate side-chains 266 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 14 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 177 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 270 ASN A 290 HIS A 337 ASN A 588 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN E 496 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN H 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.096862 restraints weight = 28932.845| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.72 r_work: 0.2951 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21175 Z= 0.182 Angle : 0.531 10.199 28832 Z= 0.276 Chirality : 0.043 0.147 2951 Planarity : 0.004 0.042 3837 Dihedral : 5.172 48.489 2836 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.50 % Allowed : 12.62 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 2577 helix: -2.33 (0.49), residues: 95 sheet: -0.02 (0.20), residues: 650 loop : -0.40 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 312 TYR 0.017 0.002 TYR L 57 PHE 0.016 0.002 PHE D 662 TRP 0.017 0.001 TRP H 66 HIS 0.010 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00434 (21173) covalent geometry : angle 0.53122 (28828) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.60660 ( 4) hydrogen bonds : bond 0.02835 ( 276) hydrogen bonds : angle 5.53094 ( 564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.7732 (m) cc_final: 0.7494 (p) REVERT: A 398 GLU cc_start: 0.8462 (mp0) cc_final: 0.7950 (mp0) REVERT: A 449 LYS cc_start: 0.7980 (mttt) cc_final: 0.7011 (mttt) REVERT: A 458 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7158 (mm-40) REVERT: A 565 GLU cc_start: 0.8031 (mp0) cc_final: 0.7753 (mp0) REVERT: A 588 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: B 456 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8057 (mp10) REVERT: B 514 ARG cc_start: 0.8082 (mtm180) cc_final: 0.5641 (mtp180) REVERT: B 562 ASN cc_start: 0.8105 (p0) cc_final: 0.7731 (p0) REVERT: C 231 ASP cc_start: 0.7729 (p0) cc_final: 0.7494 (p0) REVERT: C 567 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8337 (ptpp) REVERT: C 588 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7998 (mm-40) REVERT: C 668 ASN cc_start: 0.7404 (p0) cc_final: 0.7080 (m-40) REVERT: C 691 ASN cc_start: 0.8222 (t0) cc_final: 0.7909 (t0) REVERT: C 712 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8165 (mt-10) REVERT: C 736 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8159 (tp) REVERT: D 238 ARG cc_start: 0.7091 (tpt170) cc_final: 0.6616 (mmt90) REVERT: D 297 ASP cc_start: 0.7304 (m-30) cc_final: 0.7047 (m-30) REVERT: D 686 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: E 418 GLU cc_start: 0.7816 (pt0) cc_final: 0.7574 (pt0) REVERT: E 641 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7695 (mttt) REVERT: F 258 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7189 (tptt) REVERT: F 398 GLU cc_start: 0.4372 (OUTLIER) cc_final: 0.3691 (tm-30) REVERT: F 403 GLN cc_start: 0.7887 (tt0) cc_final: 0.7426 (tt0) REVERT: F 641 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8640 (mttm) REVERT: H 101 GLU cc_start: 0.8712 (tt0) cc_final: 0.8350 (tt0) REVERT: H 108 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7978 (mp0) outliers start: 56 outliers final: 39 residues processed: 268 average time/residue: 0.6124 time to fit residues: 185.4037 Evaluate side-chains 267 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 419 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain E residue 565 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 209 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 3 optimal weight: 0.0770 chunk 225 optimal weight: 8.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 337 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS D 585 GLN E 496 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN H 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099522 restraints weight = 28842.980| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.73 r_work: 0.2998 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21175 Z= 0.090 Angle : 0.470 11.191 28832 Z= 0.241 Chirality : 0.040 0.148 2951 Planarity : 0.004 0.035 3837 Dihedral : 4.739 52.806 2836 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.78 % Allowed : 13.24 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.15), residues: 2577 helix: -2.50 (0.46), residues: 107 sheet: 0.03 (0.20), residues: 653 loop : -0.29 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 312 TYR 0.010 0.001 TYR C 443 PHE 0.011 0.001 PHE D 662 TRP 0.015 0.001 TRP H 66 HIS 0.004 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00205 (21173) covalent geometry : angle 0.47003 (28828) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.50372 ( 4) hydrogen bonds : bond 0.02257 ( 276) hydrogen bonds : angle 5.21359 ( 564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.7762 (m) cc_final: 0.7548 (p) REVERT: A 406 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7774 (mtt-85) REVERT: A 449 LYS cc_start: 0.7965 (mttt) cc_final: 0.7089 (mttt) REVERT: A 458 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7064 (mm-40) REVERT: A 565 GLU cc_start: 0.8012 (mp0) cc_final: 0.7729 (mp0) REVERT: A 588 GLN cc_start: 0.8096 (mp10) cc_final: 0.7894 (pm20) REVERT: B 456 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8025 (mp10) REVERT: B 514 ARG cc_start: 0.8029 (mtm180) cc_final: 0.5700 (mtp180) REVERT: B 562 ASN cc_start: 0.8069 (p0) cc_final: 0.7701 (p0) REVERT: C 567 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8225 (ptpp) REVERT: C 588 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8011 (mm-40) REVERT: C 668 ASN cc_start: 0.7359 (p0) cc_final: 0.7015 (m-40) REVERT: C 691 ASN cc_start: 0.8201 (t0) cc_final: 0.7898 (t0) REVERT: C 712 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8135 (mt-10) REVERT: D 238 ARG cc_start: 0.7082 (tpt170) cc_final: 0.6575 (mmt90) REVERT: D 686 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: F 258 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7176 (tptt) REVERT: F 398 GLU cc_start: 0.4292 (OUTLIER) cc_final: 0.3774 (tm-30) REVERT: F 403 GLN cc_start: 0.7873 (tt0) cc_final: 0.7459 (tt0) REVERT: F 458 GLN cc_start: 0.7486 (mt0) cc_final: 0.7047 (mt0) REVERT: F 641 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8648 (mttm) REVERT: H 101 GLU cc_start: 0.8618 (tt0) cc_final: 0.8269 (mt-10) REVERT: H 108 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: L 63 THR cc_start: 0.8122 (m) cc_final: 0.7753 (t) outliers start: 40 outliers final: 22 residues processed: 280 average time/residue: 0.5846 time to fit residues: 185.1085 Evaluate side-chains 262 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 419 ASN Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 134 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 290 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN E 495 GLN E 496 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN H 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100142 restraints weight = 28935.660| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.73 r_work: 0.3003 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21175 Z= 0.089 Angle : 0.465 10.781 28832 Z= 0.237 Chirality : 0.040 0.147 2951 Planarity : 0.004 0.035 3837 Dihedral : 4.517 52.972 2832 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.87 % Allowed : 13.91 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2577 helix: -2.27 (0.49), residues: 101 sheet: 0.12 (0.20), residues: 662 loop : -0.20 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 550 TYR 0.011 0.001 TYR L 57 PHE 0.010 0.001 PHE E 535 TRP 0.013 0.001 TRP H 66 HIS 0.004 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00206 (21173) covalent geometry : angle 0.46485 (28828) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.48170 ( 4) hydrogen bonds : bond 0.02211 ( 276) hydrogen bonds : angle 5.05102 ( 564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 449 LYS cc_start: 0.7953 (mttt) cc_final: 0.7087 (mttt) REVERT: A 458 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7072 (mm-40) REVERT: A 565 GLU cc_start: 0.8012 (mp0) cc_final: 0.7732 (mp0) REVERT: B 456 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8021 (mp10) REVERT: B 514 ARG cc_start: 0.8022 (mtm180) cc_final: 0.5688 (mtp180) REVERT: B 562 ASN cc_start: 0.8045 (p0) cc_final: 0.7693 (p0) REVERT: C 233 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7326 (mm110) REVERT: C 588 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: C 668 ASN cc_start: 0.7413 (p0) cc_final: 0.7196 (p0) REVERT: C 691 ASN cc_start: 0.8230 (t0) cc_final: 0.7913 (t0) REVERT: C 712 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8134 (mt-10) REVERT: D 238 ARG cc_start: 0.7046 (tpt170) cc_final: 0.6778 (tpt170) REVERT: D 297 ASP cc_start: 0.7331 (m-30) cc_final: 0.7084 (m-30) REVERT: D 686 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: F 258 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7154 (tptt) REVERT: F 398 GLU cc_start: 0.4675 (OUTLIER) cc_final: 0.3874 (tm-30) REVERT: F 403 GLN cc_start: 0.7877 (tt0) cc_final: 0.7437 (tt0) REVERT: F 458 GLN cc_start: 0.7453 (mt0) cc_final: 0.7072 (mt0) REVERT: F 641 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8674 (mttm) REVERT: H 101 GLU cc_start: 0.8654 (tt0) cc_final: 0.8263 (mt-10) REVERT: H 108 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: L 63 THR cc_start: 0.8004 (m) cc_final: 0.7655 (t) outliers start: 42 outliers final: 21 residues processed: 269 average time/residue: 0.5929 time to fit residues: 180.3838 Evaluate side-chains 254 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 40 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 270 ASN A 290 HIS A 337 ASN A 588 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN D 343 GLN E 495 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS F 304 ASN H 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.096844 restraints weight = 28782.055| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.72 r_work: 0.2960 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21175 Z= 0.186 Angle : 0.530 10.645 28832 Z= 0.274 Chirality : 0.043 0.150 2951 Planarity : 0.004 0.038 3837 Dihedral : 4.753 41.869 2828 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.60 % Allowed : 14.58 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 2577 helix: -2.41 (0.48), residues: 101 sheet: 0.07 (0.20), residues: 664 loop : -0.34 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 550 TYR 0.020 0.002 TYR L 57 PHE 0.014 0.002 PHE F 535 TRP 0.014 0.002 TRP H 66 HIS 0.006 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00440 (21173) covalent geometry : angle 0.53020 (28828) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.60928 ( 4) hydrogen bonds : bond 0.02815 ( 276) hydrogen bonds : angle 5.38272 ( 564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.761 Fit side-chains REVERT: A 449 LYS cc_start: 0.8037 (mttt) cc_final: 0.7347 (mttp) REVERT: A 458 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7162 (mm-40) REVERT: A 565 GLU cc_start: 0.8003 (mp0) cc_final: 0.7721 (mp0) REVERT: B 441 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 456 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8031 (mp10) REVERT: B 514 ARG cc_start: 0.8115 (mtm180) cc_final: 0.5669 (mtp180) REVERT: B 562 ASN cc_start: 0.8120 (p0) cc_final: 0.7780 (p0) REVERT: C 233 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7311 (mm110) REVERT: C 588 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7981 (mm-40) REVERT: C 668 ASN cc_start: 0.7383 (p0) cc_final: 0.7178 (p0) REVERT: C 691 ASN cc_start: 0.8385 (t0) cc_final: 0.8061 (t0) REVERT: C 712 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8187 (mt-10) REVERT: C 736 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8287 (tp) REVERT: D 238 ARG cc_start: 0.7055 (tpt170) cc_final: 0.6778 (tpt170) REVERT: D 297 ASP cc_start: 0.7331 (m-30) cc_final: 0.7096 (m-30) REVERT: D 686 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: F 258 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7166 (tptt) REVERT: F 398 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3801 (tm-30) REVERT: F 458 GLN cc_start: 0.7459 (mt0) cc_final: 0.7089 (mt0) REVERT: F 641 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8668 (mttm) REVERT: H 101 GLU cc_start: 0.8749 (tt0) cc_final: 0.8368 (tt0) REVERT: H 108 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7959 (mp0) outliers start: 36 outliers final: 23 residues processed: 251 average time/residue: 0.6169 time to fit residues: 175.2683 Evaluate side-chains 253 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 246 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 180 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 290 HIS A 437 ASN A 588 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN D 651 ASN E 495 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS F 304 ASN F 403 GLN H 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096292 restraints weight = 29012.099| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.72 r_work: 0.2940 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21175 Z= 0.194 Angle : 0.538 10.696 28832 Z= 0.279 Chirality : 0.044 0.167 2951 Planarity : 0.004 0.042 3837 Dihedral : 4.879 41.797 2828 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.01 % Allowed : 14.36 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 2577 helix: -2.50 (0.48), residues: 101 sheet: 0.00 (0.20), residues: 642 loop : -0.42 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 550 TYR 0.021 0.002 TYR L 57 PHE 0.014 0.002 PHE F 535 TRP 0.016 0.002 TRP H 66 HIS 0.006 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00461 (21173) covalent geometry : angle 0.53811 (28828) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.64222 ( 4) hydrogen bonds : bond 0.02870 ( 276) hydrogen bonds : angle 5.50309 ( 564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.819 Fit side-chains REVERT: A 449 LYS cc_start: 0.8055 (mttt) cc_final: 0.7339 (mttp) REVERT: A 458 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7147 (mm-40) REVERT: A 565 GLU cc_start: 0.8000 (mp0) cc_final: 0.7721 (mp0) REVERT: B 441 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: B 456 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8027 (mp10) REVERT: B 514 ARG cc_start: 0.8104 (mtm180) cc_final: 0.5641 (mtp180) REVERT: B 562 ASN cc_start: 0.8139 (p0) cc_final: 0.7786 (p0) REVERT: B 593 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8679 (t) REVERT: C 233 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7305 (mm110) REVERT: C 588 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7975 (mm-40) REVERT: C 691 ASN cc_start: 0.8401 (t0) cc_final: 0.8081 (t0) REVERT: C 712 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 736 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8295 (tp) REVERT: D 238 ARG cc_start: 0.7066 (tpt170) cc_final: 0.6809 (tpt170) REVERT: D 686 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: F 258 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7190 (tptt) REVERT: F 332 LYS cc_start: 0.7434 (ptmm) cc_final: 0.7129 (ttpp) REVERT: F 398 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4165 (tm-30) REVERT: F 403 GLN cc_start: 0.7885 (tt0) cc_final: 0.7438 (tt0) REVERT: F 458 GLN cc_start: 0.7454 (mt0) cc_final: 0.7070 (mt0) REVERT: F 641 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8663 (mttm) REVERT: H 101 GLU cc_start: 0.8783 (tt0) cc_final: 0.8382 (tt0) REVERT: H 108 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7976 (mp0) outliers start: 45 outliers final: 29 residues processed: 259 average time/residue: 0.5837 time to fit residues: 171.2889 Evaluate side-chains 259 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 657 ASP Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 559 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 67 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 140 optimal weight: 7.9990 chunk 150 optimal weight: 0.0020 chunk 215 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 290 HIS A 337 ASN A 588 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN E 495 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS F 304 ASN H 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097358 restraints weight = 29013.319| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.73 r_work: 0.2971 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21175 Z= 0.120 Angle : 0.500 11.482 28832 Z= 0.256 Chirality : 0.041 0.145 2951 Planarity : 0.004 0.043 3837 Dihedral : 4.673 42.688 2828 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.69 % Allowed : 14.62 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 2577 helix: -2.46 (0.48), residues: 101 sheet: 0.04 (0.20), residues: 637 loop : -0.37 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 550 TYR 0.015 0.001 TYR L 57 PHE 0.011 0.001 PHE D 662 TRP 0.017 0.001 TRP H 66 HIS 0.004 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00281 (21173) covalent geometry : angle 0.50049 (28828) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.51457 ( 4) hydrogen bonds : bond 0.02504 ( 276) hydrogen bonds : angle 5.33246 ( 564) =============================================================================== Job complete usr+sys time: 6693.78 seconds wall clock time: 114 minutes 53.30 seconds (6893.30 seconds total)