Starting phenix.real_space_refine on Tue May 20 13:16:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7k_44314/05_2025/9b7k_44314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7k_44314/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7k_44314/05_2025/9b7k_44314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7k_44314/05_2025/9b7k_44314.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7k_44314/05_2025/9b7k_44314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7k_44314/05_2025/9b7k_44314.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.89, per 1000 atoms: 0.58 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: 4.64 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.36 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: 5.89 Time building geometry restraints manager: 5.48 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 43.340 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.790 ------------------------------------------------------------------------------- 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 : 14.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.027 0.002 TRP F 228 HIS 0.012 0.002 HIS F 290 PHE 0.021 0.002 PHE C 367 TYR 0.024 0.002 TYR F 705 ARG 0.011 0.001 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.24793 ( 276) hydrogen bonds : angle 8.63853 ( 564) SS BOND : bond 0.00360 ( 2) SS BOND : angle 0.27376 ( 4) covalent geometry : bond 0.00548 (21173) covalent geometry : angle 0.92776 (28828) *********************** 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 : 2.381 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: 1.2949 time to fit residues: 645.5576 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 : 2.395 ------------------------------------------------------------------------------- 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 217 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 131 optimal weight: 0.0000 chunk 104 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 233 optimal weight: 3.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 452 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 321 GLN C 497 ASN C 515 ASN C 646 GLN C 651 ASN C 673 GLN C 704 ASN D 229 HIS D 262 ASN D 343 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN 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 608 GLN E 624 HIS F 229 HIS F 255 HIS F 403 GLN F 412 GLN F 430 GLN F 452 ASN F 470 ASN F 546 GLN F 608 GLN F 624 HIS F 673 GLN F 700 GLN H 22 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103589 restraints weight = 28400.473| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.68 r_work: 0.3063 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21175 Z= 0.117 Angle : 0.557 11.136 28832 Z= 0.292 Chirality : 0.043 0.157 2951 Planarity : 0.004 0.035 3837 Dihedral : 6.145 57.349 2870 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.99 % Allowed : 9.32 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 2577 helix: -3.18 (0.37), residues: 107 sheet: -0.09 (0.17), residues: 719 loop : -0.33 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 228 HIS 0.006 0.001 HIS F 290 PHE 0.015 0.001 PHE C 367 TYR 0.014 0.001 TYR A 674 ARG 0.005 0.001 ARG D 485 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 276) hydrogen bonds : angle 6.24718 ( 564) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.55577 ( 4) covalent geometry : bond 0.00261 (21173) covalent geometry : angle 0.55651 (28828) *********************** 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 348 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 2.536 Fit side-chains REVERT: A 300 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7253 (ttp-110) REVERT: A 333 THR cc_start: 0.7656 (m) cc_final: 0.7273 (p) REVERT: A 343 GLN cc_start: 0.8741 (mt0) cc_final: 0.8335 (mt0) REVERT: A 398 GLU cc_start: 0.8304 (mp0) cc_final: 0.8056 (mp0) REVERT: A 449 LYS cc_start: 0.7809 (mttt) cc_final: 0.7031 (mttt) REVERT: A 546 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7476 (mt0) REVERT: A 682 GLU cc_start: 0.7748 (tt0) cc_final: 0.7136 (tm-30) REVERT: B 441 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: B 456 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7995 (mm110) REVERT: B 514 ARG cc_start: 0.7894 (mtm180) cc_final: 0.5772 (mtp180) REVERT: C 485 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6153 (ttp-170) REVERT: C 605 MET cc_start: 0.9192 (mtt) cc_final: 0.8919 (mtt) REVERT: C 668 ASN cc_start: 0.7591 (p0) cc_final: 0.7198 (m-40) REVERT: D 297 ASP cc_start: 0.7262 (m-30) cc_final: 0.7035 (m-30) REVERT: D 316 LYS cc_start: 0.8107 (mttt) cc_final: 0.7409 (mtpm) REVERT: D 686 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: E 641 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7518 (mttt) REVERT: F 258 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7451 (tptt) REVERT: F 387 GLN cc_start: 0.8204 (mt0) cc_final: 0.7997 (mt0) REVERT: F 641 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8597 (mttm) REVERT: H 101 GLU cc_start: 0.8606 (tt0) cc_final: 0.8272 (tt0) REVERT: H 108 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: L 63 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7816 (t) outliers start: 67 outliers final: 24 residues processed: 323 average time/residue: 1.3908 time to fit residues: 508.2750 Evaluate side-chains 260 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 485 ARG 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 491 THR Chi-restraints excluded: chain D residue 494 THR 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 F residue 239 VAL 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 141 GLN Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain L residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 85 optimal weight: 50.0000 chunk 60 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 184 optimal weight: 40.0000 chunk 219 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 290 HIS A 337 ASN A 588 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 428 HIS C 452 ASN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 GLN D 376 GLN E 496 ASN ** 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 = 0.3334 r_free = 0.3334 target = 0.118272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.096492 restraints weight = 28928.211| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.73 r_work: 0.2958 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21175 Z= 0.230 Angle : 0.601 12.219 28832 Z= 0.315 Chirality : 0.046 0.158 2951 Planarity : 0.005 0.045 3837 Dihedral : 5.669 47.812 2838 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.34 % Allowed : 9.76 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2577 helix: -2.88 (0.41), residues: 107 sheet: -0.08 (0.19), residues: 653 loop : -0.45 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 66 HIS 0.018 0.001 HIS F 290 PHE 0.016 0.002 PHE E 535 TYR 0.017 0.002 TYR B 443 ARG 0.007 0.001 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 276) hydrogen bonds : angle 6.01538 ( 564) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.59883 ( 4) covalent geometry : bond 0.00555 (21173) covalent geometry : angle 0.60128 (28828) *********************** 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 309 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 2.501 Fit side-chains REVERT: A 300 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7275 (ttp-110) REVERT: A 333 THR cc_start: 0.7675 (m) cc_final: 0.7332 (p) REVERT: A 449 LYS cc_start: 0.7940 (mttt) cc_final: 0.7100 (mttt) REVERT: A 546 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7529 (mt0) REVERT: A 682 GLU cc_start: 0.7892 (tt0) cc_final: 0.7220 (tm-30) REVERT: B 441 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: B 514 ARG cc_start: 0.8043 (mtm180) cc_final: 0.5759 (mtp180) REVERT: B 524 MET cc_start: 0.8720 (mtp) cc_final: 0.8493 (mtm) REVERT: C 668 ASN cc_start: 0.7532 (p0) cc_final: 0.7184 (m-40) REVERT: C 736 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8230 (tp) REVERT: D 297 ASP cc_start: 0.7254 (m-30) cc_final: 0.6997 (m-30) REVERT: D 686 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: E 641 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7638 (mtpt) REVERT: F 258 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7185 (tptt) REVERT: F 387 GLN cc_start: 0.8191 (mt0) cc_final: 0.7808 (mt0) REVERT: F 398 GLU cc_start: 0.4576 (OUTLIER) cc_final: 0.3708 (tm-30) REVERT: F 531 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: F 641 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8645 (mttm) REVERT: H 44 SER cc_start: 0.8656 (p) cc_final: 0.8448 (m) REVERT: H 101 GLU cc_start: 0.8675 (tt0) cc_final: 0.8308 (tt0) REVERT: H 108 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7890 (mp0) outliers start: 75 outliers final: 42 residues processed: 282 average time/residue: 1.3697 time to fit residues: 436.9335 Evaluate side-chains 269 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 2.255 ------------------------------------------------------------------------------- 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 465 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 441 ASP 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 343 GLN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 551 ASP 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 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 540 SER Chi-restraints excluded: chain D residue 563 GLU 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 538 SER Chi-restraints excluded: chain E residue 559 MET 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 531 GLU 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 143 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 66 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 437 ASN A 588 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097780 restraints weight = 28935.847| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.68 r_work: 0.2969 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21175 Z= 0.161 Angle : 0.533 10.952 28832 Z= 0.277 Chirality : 0.043 0.145 2951 Planarity : 0.004 0.044 3837 Dihedral : 5.422 54.939 2838 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.30 % Allowed : 11.01 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2577 helix: -2.72 (0.44), residues: 107 sheet: -0.04 (0.19), residues: 658 loop : -0.41 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 66 HIS 0.010 0.001 HIS F 290 PHE 0.013 0.002 PHE E 535 TYR 0.012 0.002 TYR F 701 ARG 0.006 0.001 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 276) hydrogen bonds : angle 5.73079 ( 564) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.69787 ( 4) covalent geometry : bond 0.00381 (21173) covalent geometry : angle 0.53280 (28828) *********************** 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 315 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 241 time to evaluate : 2.400 Fit side-chains REVERT: A 300 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7239 (ttp-110) REVERT: A 333 THR cc_start: 0.7702 (m) cc_final: 0.7418 (p) REVERT: A 449 LYS cc_start: 0.7998 (mttt) cc_final: 0.7040 (mttt) REVERT: A 546 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7524 (mt0) REVERT: A 565 GLU cc_start: 0.8059 (mp0) cc_final: 0.7791 (mp0) REVERT: A 682 GLU cc_start: 0.7885 (tt0) cc_final: 0.7179 (tm-30) REVERT: B 441 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 514 ARG cc_start: 0.8088 (mtm180) cc_final: 0.5758 (mtp180) REVERT: B 562 ASN cc_start: 0.8221 (p0) cc_final: 0.7800 (p0) REVERT: C 588 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8011 (mm-40) REVERT: C 668 ASN cc_start: 0.7473 (p0) cc_final: 0.7154 (m-40) REVERT: C 682 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: C 736 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8123 (tp) REVERT: D 297 ASP cc_start: 0.7357 (m-30) cc_final: 0.7094 (m-30) REVERT: D 529 GLU cc_start: 0.7838 (tt0) cc_final: 0.7198 (pt0) REVERT: D 686 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: E 641 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7683 (mttt) REVERT: F 238 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7826 (mtt180) REVERT: F 258 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7195 (tptt) REVERT: F 387 GLN cc_start: 0.8184 (mt0) cc_final: 0.7796 (mt0) REVERT: F 398 GLU cc_start: 0.4352 (OUTLIER) cc_final: 0.3781 (tm-30) REVERT: F 403 GLN cc_start: 0.7926 (tt0) cc_final: 0.7472 (tt0) REVERT: F 641 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8644 (mttm) REVERT: H 101 GLU cc_start: 0.8643 (tt0) cc_final: 0.8314 (tt0) REVERT: H 108 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: L 63 THR cc_start: 0.8406 (m) cc_final: 0.7917 (t) outliers start: 74 outliers final: 39 residues processed: 287 average time/residue: 1.3324 time to fit residues: 434.7942 Evaluate side-chains 271 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 2.376 ------------------------------------------------------------------------------- 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 B residue 441 ASP Chi-restraints excluded: chain B residue 559 MET 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 448 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 682 GLU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 148 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- 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 437 ASN A 588 GLN A 673 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3320 r_free = 0.3320 target = 0.117096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.095584 restraints weight = 29094.769| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.68 r_work: 0.2924 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 21175 Z= 0.238 Angle : 0.582 11.064 28832 Z= 0.304 Chirality : 0.045 0.165 2951 Planarity : 0.005 0.053 3837 Dihedral : 5.664 57.787 2837 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.21 % Allowed : 12.17 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2577 helix: -2.64 (0.46), residues: 101 sheet: -0.11 (0.19), residues: 658 loop : -0.51 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 66 HIS 0.013 0.001 HIS F 290 PHE 0.016 0.002 PHE F 501 TYR 0.020 0.002 TYR L 57 ARG 0.006 0.001 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 276) hydrogen bonds : angle 5.84277 ( 564) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.76675 ( 4) covalent geometry : bond 0.00568 (21173) covalent geometry : angle 0.58246 (28828) *********************** 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 297 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 225 time to evaluate : 2.501 Fit side-chains REVERT: A 300 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7420 (ttp-110) REVERT: A 333 THR cc_start: 0.7753 (m) cc_final: 0.7478 (p) REVERT: A 449 LYS cc_start: 0.8101 (mttt) cc_final: 0.7143 (mttt) REVERT: A 546 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7648 (mt0) REVERT: A 565 GLU cc_start: 0.8041 (mp0) cc_final: 0.7782 (mp0) REVERT: A 588 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: A 682 GLU cc_start: 0.8009 (tt0) cc_final: 0.7246 (tm-30) REVERT: B 514 ARG cc_start: 0.8140 (mtm180) cc_final: 0.5669 (mtp180) REVERT: B 562 ASN cc_start: 0.8267 (p0) cc_final: 0.7888 (p0) REVERT: B 564 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: C 554 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: C 567 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8382 (ptpp) REVERT: C 588 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: C 668 ASN cc_start: 0.7404 (p0) cc_final: 0.7089 (m-40) REVERT: C 682 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: C 736 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8209 (tp) REVERT: D 297 ASP cc_start: 0.7344 (m-30) cc_final: 0.7102 (m-30) REVERT: D 529 GLU cc_start: 0.7790 (tt0) cc_final: 0.7150 (pt0) REVERT: D 686 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: E 641 LYS cc_start: 0.8421 (mtmt) cc_final: 0.7742 (mttt) REVERT: F 238 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7812 (mpt-90) REVERT: F 258 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7225 (tptt) REVERT: F 387 GLN cc_start: 0.8217 (mt0) cc_final: 0.7852 (mt0) REVERT: F 398 GLU cc_start: 0.4585 (OUTLIER) cc_final: 0.3837 (tm-30) REVERT: F 403 GLN cc_start: 0.7911 (tt0) cc_final: 0.7489 (tt0) REVERT: F 458 GLN cc_start: 0.7631 (mt0) cc_final: 0.7405 (mt0) REVERT: F 641 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8683 (mttm) REVERT: H 101 GLU cc_start: 0.8677 (tt0) cc_final: 0.8346 (tt0) REVERT: H 108 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7908 (mp0) outliers start: 72 outliers final: 42 residues processed: 275 average time/residue: 1.3231 time to fit residues: 414.3665 Evaluate side-chains 269 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 2.346 ------------------------------------------------------------------------------- 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 437 ASN 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 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 343 GLN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 516 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 567 LYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 682 GLU 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 34 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 437 ASN A 588 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN H 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095729 restraints weight = 29057.025| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.73 r_work: 0.2940 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2350 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= 0.204 Angle : 0.556 10.969 28832 Z= 0.290 Chirality : 0.044 0.164 2951 Planarity : 0.004 0.055 3837 Dihedral : 5.527 49.743 2837 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.17 % Allowed : 12.57 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2577 helix: -2.63 (0.46), residues: 101 sheet: -0.15 (0.20), residues: 648 loop : -0.53 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 66 HIS 0.010 0.001 HIS F 290 PHE 0.014 0.002 PHE E 535 TYR 0.016 0.002 TYR L 57 ARG 0.004 0.001 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 276) hydrogen bonds : angle 5.76532 ( 564) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.70863 ( 4) covalent geometry : bond 0.00486 (21173) covalent geometry : angle 0.55623 (28828) *********************** 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 291 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 2.505 Fit side-chains REVERT: A 304 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7472 (m110) REVERT: A 333 THR cc_start: 0.7713 (m) cc_final: 0.7448 (p) REVERT: A 449 LYS cc_start: 0.8077 (mttt) cc_final: 0.7088 (mttt) REVERT: A 458 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7203 (mm-40) REVERT: A 565 GLU cc_start: 0.8036 (mp0) cc_final: 0.7756 (mp0) REVERT: A 682 GLU cc_start: 0.8009 (tt0) cc_final: 0.7197 (tm-30) REVERT: B 514 ARG cc_start: 0.8136 (mtm180) cc_final: 0.5573 (mtp180) REVERT: B 562 ASN cc_start: 0.8189 (p0) cc_final: 0.7806 (p0) REVERT: B 564 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: C 546 GLN cc_start: 0.7725 (tt0) cc_final: 0.7422 (tt0) REVERT: C 567 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8359 (ptpp) REVERT: C 588 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7995 (mm-40) REVERT: C 668 ASN cc_start: 0.7409 (p0) cc_final: 0.7038 (m-40) REVERT: C 682 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: C 691 ASN cc_start: 0.8274 (t0) cc_final: 0.7993 (t0) REVERT: C 736 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8111 (tp) REVERT: D 529 GLU cc_start: 0.7775 (tt0) cc_final: 0.7101 (pt0) REVERT: D 686 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: F 238 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7795 (mpt-90) REVERT: F 258 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7192 (tptt) REVERT: F 387 GLN cc_start: 0.8197 (mt0) cc_final: 0.7841 (mt0) REVERT: F 398 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.4107 (tm-30) REVERT: F 403 GLN cc_start: 0.7907 (tt0) cc_final: 0.7467 (tt0) REVERT: F 458 GLN cc_start: 0.7634 (mt0) cc_final: 0.7369 (mt0) REVERT: F 641 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8661 (mttm) REVERT: H 101 GLU cc_start: 0.8668 (tt0) cc_final: 0.8325 (tt0) REVERT: H 108 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7899 (mp0) outliers start: 71 outliers final: 44 residues processed: 270 average time/residue: 1.3749 time to fit residues: 422.7838 Evaluate side-chains 269 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 494 THR 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 343 GLN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 538 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 682 GLU Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 712 GLU 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 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 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 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 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 44 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 177 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN H 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097157 restraints weight = 28929.281| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.68 r_work: 0.2944 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21175 Z= 0.146 Angle : 0.516 10.772 28832 Z= 0.267 Chirality : 0.042 0.145 2951 Planarity : 0.004 0.048 3837 Dihedral : 5.221 51.000 2837 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.67 % Allowed : 12.80 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 2577 helix: -2.58 (0.47), residues: 101 sheet: -0.13 (0.20), residues: 650 loop : -0.47 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 66 HIS 0.007 0.001 HIS F 290 PHE 0.012 0.001 PHE E 535 TYR 0.013 0.001 TYR F 701 ARG 0.004 0.000 ARG F 238 Details of bonding type rmsd hydrogen bonds : bond 0.02632 ( 276) hydrogen bonds : angle 5.56169 ( 564) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.57603 ( 4) covalent geometry : bond 0.00347 (21173) covalent geometry : angle 0.51566 (28828) *********************** 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 292 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 2.526 Fit side-chains REVERT: A 333 THR cc_start: 0.7798 (m) cc_final: 0.7546 (p) REVERT: A 449 LYS cc_start: 0.8137 (mttt) cc_final: 0.7094 (mttt) REVERT: A 458 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7167 (mm-40) REVERT: A 565 GLU cc_start: 0.8017 (mp0) cc_final: 0.7750 (mp0) REVERT: A 682 GLU cc_start: 0.8017 (tt0) cc_final: 0.7746 (tt0) REVERT: B 441 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: B 514 ARG cc_start: 0.8117 (mtm180) cc_final: 0.5679 (mtp180) REVERT: B 562 ASN cc_start: 0.8182 (p0) cc_final: 0.7810 (p0) REVERT: B 564 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: C 233 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7355 (mm110) REVERT: C 337 ASN cc_start: 0.8132 (t0) cc_final: 0.7930 (t0) REVERT: C 588 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: C 668 ASN cc_start: 0.7370 (p0) cc_final: 0.6997 (m-40) REVERT: C 682 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7647 (pp20) REVERT: C 691 ASN cc_start: 0.8271 (t0) cc_final: 0.8009 (t0) REVERT: C 736 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8108 (tp) REVERT: D 529 GLU cc_start: 0.7795 (tt0) cc_final: 0.7134 (pt0) REVERT: D 686 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: F 258 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7232 (tptt) REVERT: F 332 LYS cc_start: 0.7406 (ptmm) cc_final: 0.6926 (ttpp) REVERT: F 387 GLN cc_start: 0.8273 (mt0) cc_final: 0.7929 (mt0) REVERT: F 398 GLU cc_start: 0.4445 (OUTLIER) cc_final: 0.4061 (tm-30) REVERT: F 403 GLN cc_start: 0.7903 (tt0) cc_final: 0.7477 (tt0) REVERT: F 458 GLN cc_start: 0.7664 (mt0) cc_final: 0.7423 (mt0) REVERT: F 641 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8692 (mttm) REVERT: H 101 GLU cc_start: 0.8633 (tt0) cc_final: 0.8326 (tt0) REVERT: H 108 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: L 63 THR cc_start: 0.8462 (m) cc_final: 0.8069 (t) outliers start: 60 outliers final: 34 residues processed: 274 average time/residue: 1.2455 time to fit residues: 389.9047 Evaluate side-chains 268 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 676 THR Chi-restraints excluded: chain B residue 441 ASP 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 343 GLN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 712 GLU 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 494 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 686 GLU 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 E residue 601 ILE Chi-restraints excluded: chain F residue 235 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 184 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 196 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096421 restraints weight = 29024.834| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.72 r_work: 0.2950 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2483 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= 0.174 Angle : 0.531 11.216 28832 Z= 0.275 Chirality : 0.043 0.153 2951 Planarity : 0.004 0.048 3837 Dihedral : 5.199 50.799 2836 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.59 % Allowed : 13.11 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2577 helix: -2.54 (0.47), residues: 101 sheet: -0.15 (0.20), residues: 644 loop : -0.49 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 66 HIS 0.005 0.001 HIS F 292 PHE 0.017 0.002 PHE D 662 TYR 0.020 0.002 TYR L 57 ARG 0.003 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 276) hydrogen bonds : angle 5.57515 ( 564) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.67277 ( 4) covalent geometry : bond 0.00415 (21173) covalent geometry : angle 0.53130 (28828) *********************** 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: 58 poor density : 226 time to evaluate : 2.257 Fit side-chains REVERT: A 333 THR cc_start: 0.7796 (m) cc_final: 0.7555 (p) REVERT: A 449 LYS cc_start: 0.8103 (mttt) cc_final: 0.7348 (mttp) REVERT: A 458 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7077 (mm-40) REVERT: A 682 GLU cc_start: 0.7978 (tt0) cc_final: 0.7722 (tt0) REVERT: B 514 ARG cc_start: 0.8112 (mtm180) cc_final: 0.5646 (mtp180) REVERT: B 562 ASN cc_start: 0.8164 (p0) cc_final: 0.7793 (p0) REVERT: B 564 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7095 (pp20) REVERT: C 233 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7352 (mm110) REVERT: C 337 ASN cc_start: 0.8085 (t0) cc_final: 0.7843 (t0) REVERT: C 567 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8344 (ptpp) REVERT: C 588 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: C 668 ASN cc_start: 0.7353 (p0) cc_final: 0.7140 (p0) REVERT: C 682 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: C 691 ASN cc_start: 0.8233 (t0) cc_final: 0.7981 (t0) REVERT: C 736 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8109 (tp) REVERT: D 529 GLU cc_start: 0.7771 (tt0) cc_final: 0.7097 (pt0) REVERT: D 686 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: F 258 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7204 (tptt) REVERT: F 300 ARG cc_start: 0.8959 (ttm170) cc_final: 0.8745 (mtm-85) REVERT: F 387 GLN cc_start: 0.8243 (mt0) cc_final: 0.7900 (mt0) REVERT: F 398 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.3691 (tm-30) REVERT: F 403 GLN cc_start: 0.7922 (tt0) cc_final: 0.7475 (tt0) REVERT: F 458 GLN cc_start: 0.7649 (mm110) cc_final: 0.7394 (mt0) REVERT: F 641 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8690 (mttm) REVERT: H 101 GLU cc_start: 0.8653 (tt0) cc_final: 0.8322 (tt0) REVERT: H 108 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: L 63 THR cc_start: 0.8460 (m) cc_final: 0.8012 (t) outliers start: 58 outliers final: 40 residues processed: 269 average time/residue: 1.3455 time to fit residues: 412.2018 Evaluate side-chains 270 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL 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 676 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 441 ASP 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 343 GLN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 538 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 682 GLU Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain D residue 235 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 494 THR 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 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 E residue 601 ILE Chi-restraints excluded: chain F residue 235 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 174 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096188 restraints weight = 28985.546| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.72 r_work: 0.2931 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21175 Z= 0.186 Angle : 0.539 11.143 28832 Z= 0.278 Chirality : 0.043 0.167 2951 Planarity : 0.004 0.048 3837 Dihedral : 5.171 51.164 2833 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.67 % Allowed : 13.02 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2577 helix: -2.52 (0.47), residues: 101 sheet: -0.14 (0.20), residues: 649 loop : -0.51 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 66 HIS 0.005 0.001 HIS F 292 PHE 0.013 0.002 PHE E 535 TYR 0.018 0.002 TYR L 57 ARG 0.003 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 276) hydrogen bonds : angle 5.59411 ( 564) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.65553 ( 4) covalent geometry : bond 0.00445 (21173) covalent geometry : angle 0.53890 (28828) *********************** 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 277 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 2.535 Fit side-chains REVERT: A 304 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7513 (m110) REVERT: A 333 THR cc_start: 0.7784 (m) cc_final: 0.7540 (p) REVERT: A 449 LYS cc_start: 0.8076 (mttt) cc_final: 0.7134 (mttp) REVERT: A 458 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7047 (mm-40) REVERT: A 682 GLU cc_start: 0.7975 (tt0) cc_final: 0.7701 (tt0) REVERT: B 441 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 514 ARG cc_start: 0.8115 (mtm180) cc_final: 0.5620 (mtp180) REVERT: B 562 ASN cc_start: 0.8156 (p0) cc_final: 0.7783 (p0) REVERT: B 564 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: C 233 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7335 (mm110) REVERT: C 337 ASN cc_start: 0.8094 (t0) cc_final: 0.7855 (t0) REVERT: C 567 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8343 (ptpp) REVERT: C 588 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: C 668 ASN cc_start: 0.7341 (p0) cc_final: 0.7133 (p0) REVERT: C 682 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: C 691 ASN cc_start: 0.8324 (t0) cc_final: 0.8038 (t0) REVERT: C 736 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8146 (tp) REVERT: D 529 GLU cc_start: 0.7772 (tt0) cc_final: 0.7074 (pt0) REVERT: D 686 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: F 258 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7168 (tptt) REVERT: F 300 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8660 (mtm-85) REVERT: F 332 LYS cc_start: 0.7410 (ptmm) cc_final: 0.6906 (ttpp) REVERT: F 387 GLN cc_start: 0.8224 (mt0) cc_final: 0.7844 (mt0) REVERT: F 398 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3979 (tm-30) REVERT: F 403 GLN cc_start: 0.7931 (tt0) cc_final: 0.7462 (tt0) REVERT: F 458 GLN cc_start: 0.7664 (mm110) cc_final: 0.7424 (mt0) REVERT: F 641 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8687 (mttm) REVERT: H 101 GLU cc_start: 0.8660 (tt0) cc_final: 0.8310 (tt0) REVERT: H 108 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: L 63 THR cc_start: 0.8460 (m) cc_final: 0.7995 (t) outliers start: 60 outliers final: 43 residues processed: 261 average time/residue: 1.2991 time to fit residues: 386.8513 Evaluate side-chains 268 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 494 THR 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 564 GLU 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 242 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 538 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 682 GLU Chi-restraints excluded: chain C residue 712 GLU 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 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 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 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 E residue 601 ILE Chi-restraints excluded: chain F residue 235 LEU 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 H residue 56 VAL Chi-restraints excluded: chain H residue 88 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 243 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.098882 restraints weight = 28899.522| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.72 r_work: 0.2981 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2595 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= 0.093 Angle : 0.481 11.304 28832 Z= 0.246 Chirality : 0.040 0.146 2951 Planarity : 0.004 0.040 3837 Dihedral : 4.729 55.120 2833 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.60 % Allowed : 14.13 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 2577 helix: -2.53 (0.46), residues: 107 sheet: -0.06 (0.20), residues: 652 loop : -0.37 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 66 HIS 0.003 0.001 HIS D 290 PHE 0.011 0.001 PHE D 662 TYR 0.012 0.001 TYR L 57 ARG 0.003 0.000 ARG C 730 Details of bonding type rmsd hydrogen bonds : bond 0.02267 ( 276) hydrogen bonds : angle 5.25202 ( 564) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.48765 ( 4) covalent geometry : bond 0.00214 (21173) covalent geometry : angle 0.48139 (28828) ********************** 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 275 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 2.331 Fit side-chains REVERT: A 304 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7504 (m110) REVERT: A 449 LYS cc_start: 0.8031 (mttt) cc_final: 0.7283 (mttp) REVERT: A 458 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7061 (mm-40) REVERT: A 565 GLU cc_start: 0.8004 (mp0) cc_final: 0.7717 (mp0) REVERT: A 682 GLU cc_start: 0.7994 (tt0) cc_final: 0.7728 (tt0) REVERT: B 456 GLN cc_start: 0.8378 (mm110) cc_final: 0.8010 (mp10) REVERT: B 514 ARG cc_start: 0.8045 (mtm180) cc_final: 0.5616 (mtp180) REVERT: B 562 ASN cc_start: 0.8097 (p0) cc_final: 0.7754 (p0) REVERT: B 564 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7002 (pp20) REVERT: B 641 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8247 (ttpp) REVERT: C 233 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7329 (mm110) REVERT: C 567 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8243 (ptpp) REVERT: C 588 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: C 668 ASN cc_start: 0.7330 (p0) cc_final: 0.7120 (p0) REVERT: C 682 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: C 691 ASN cc_start: 0.8245 (t0) cc_final: 0.7953 (t0) REVERT: C 712 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8188 (mt-10) REVERT: D 529 GLU cc_start: 0.7763 (tt0) cc_final: 0.7117 (pt0) REVERT: F 258 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7143 (tptt) REVERT: F 332 LYS cc_start: 0.7390 (ptmm) cc_final: 0.7101 (ttpp) REVERT: F 387 GLN cc_start: 0.8347 (mt0) cc_final: 0.8012 (mt0) REVERT: F 403 GLN cc_start: 0.7925 (tt0) cc_final: 0.7461 (tt0) REVERT: F 445 TYR cc_start: 0.8227 (m-80) cc_final: 0.8011 (m-80) REVERT: F 458 GLN cc_start: 0.7605 (mm110) cc_final: 0.7378 (mt0) REVERT: F 641 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8683 (mttm) REVERT: H 101 GLU cc_start: 0.8665 (tt0) cc_final: 0.8295 (tt0) REVERT: H 108 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: L 63 THR cc_start: 0.8128 (m) cc_final: 0.7790 (t) outliers start: 36 outliers final: 20 residues processed: 264 average time/residue: 1.2647 time to fit residues: 380.2594 Evaluate side-chains 248 residues out of total 2243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 564 GLU 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 538 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 682 GLU Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain E residue 461 LEU 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 564 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 143 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 585 GLN E 495 GLN E 496 ASN ** 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 = 0.3357 r_free = 0.3357 target = 0.119917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098440 restraints weight = 28889.063| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.73 r_work: 0.2974 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21175 Z= 0.113 Angle : 0.487 11.089 28832 Z= 0.249 Chirality : 0.041 0.144 2951 Planarity : 0.004 0.041 3837 Dihedral : 4.677 54.096 2831 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.56 % Allowed : 14.31 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2577 helix: -2.34 (0.49), residues: 101 sheet: -0.02 (0.20), residues: 652 loop : -0.34 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 66 HIS 0.003 0.001 HIS D 290 PHE 0.011 0.001 PHE E 535 TYR 0.015 0.001 TYR L 57 ARG 0.002 0.000 ARG D 550 Details of bonding type rmsd hydrogen bonds : bond 0.02384 ( 276) hydrogen bonds : angle 5.20374 ( 564) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.51990 ( 4) covalent geometry : bond 0.00267 (21173) covalent geometry : angle 0.48700 (28828) =============================================================================== Job complete usr+sys time: 14881.04 seconds wall clock time: 256 minutes 47.77 seconds (15407.77 seconds total)