Starting phenix.real_space_refine on Sun Aug 24 06:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7n_44317/08_2025/9b7n_44317.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7n_44317/08_2025/9b7n_44317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b7n_44317/08_2025/9b7n_44317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7n_44317/08_2025/9b7n_44317.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7n_44317/08_2025/9b7n_44317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7n_44317/08_2025/9b7n_44317.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 11578 2.51 5 N 3181 2.21 5 O 3523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18350 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2985 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 347} Chain breaks: 3 Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1359 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 163} Chain breaks: 1 Chain: "C" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3959 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 462} Chain breaks: 2 Chain: "D" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2977 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 346} Chain breaks: 3 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1359 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 163} Chain breaks: 1 Chain: "F" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3959 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 462} Chain breaks: 2 Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 779 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Time building chain proxies: 4.67, per 1000 atoms: 0.25 Number of scatterers: 18350 At special positions: 0 Unit cell: (155.852, 124.35, 96.164, 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 68 16.00 O 3523 8.00 N 3181 7.00 C 11578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 110 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 812.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4262 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 53 sheets defined 6.4% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 563 through 569 removed outlier: 4.425A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.835A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.263A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.599A 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 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 564 through 569 removed outlier: 4.105A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 396 through 400 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 563 through 569 removed outlier: 4.200A pdb=" N THR D 568 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 569 removed outlier: 4.312A 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 262 through 266 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.204A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.528A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 568 removed outlier: 4.277A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 105 removed outlier: 3.753A pdb=" N PHE L 105 " --> pdb=" O PRO L 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 249 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 241 through 249 current: chain 'A' and resid 335 through 336 No H-bonds generated for sheet with id=AA1 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 383 through 384 Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.282A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 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: 4.032A 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 553 through 554 Processing sheet with id=AB1, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.996A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 619 through 621 Processing sheet with id=AB3, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.344A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 451 removed outlier: 6.825A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 450 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.373A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB7, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB8, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AB9, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.936A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC1, 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 249 current: chain 'C' and resid 335 through 336 Processing sheet with id=AC2, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AC3, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.446A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 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 removed outlier: 6.083A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 243 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 243 through 249 current: chain 'D' and resid 335 through 336 No H-bonds generated for sheet with id=AC8 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 479 through 480 removed outlier: 6.218A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD3, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD4, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.072A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD6, first strand: chain 'D' and resid 578 through 581 removed outlier: 3.957A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.201A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 627 through 629 removed outlier: 4.090A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 445 through 449 removed outlier: 6.663A pdb=" N LYS E 462 " --> pdb=" O SER E 448 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.094A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET E 605 " --> pdb=" O PHE F 629 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE4, first strand: chain 'E' and resid 508 through 511 Processing sheet with id=AE5, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.095A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 335 through 336 Processing sheet with id=AE7, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE8, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.378A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 445 through 451 removed outlier: 5.824A pdb=" N LEU F 447 " --> pdb=" O SER F 464 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER F 464 " --> pdb=" O LEU F 447 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE F 451 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR F 460 " --> pdb=" O ILE F 451 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AF2, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AF3, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AF4, first strand: chain 'F' and resid 619 through 621 removed outlier: 6.183A pdb=" N ALA F 620 " --> pdb=" O MET F 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 26 through 28 removed outlier: 3.641A pdb=" N ASP L 92 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 75 through 76 removed outlier: 6.470A pdb=" N TRP L 57 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR L 71 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL L 55 " --> pdb=" O TYR L 71 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AF8, first strand: chain 'H' and resid 51 through 58 removed outlier: 6.686A pdb=" N MET H 53 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 134 through 136 241 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5996 1.34 - 1.46: 3924 1.46 - 1.58: 8841 1.58 - 1.69: 0 1.69 - 1.81: 118 Bond restraints: 18879 Sorted by residual: bond pdb=" C PRO F 365 " pdb=" O PRO F 365 " ideal model delta sigma weight residual 1.246 1.229 0.017 8.50e-03 1.38e+04 3.92e+00 bond pdb=" CA ASN D 287 " pdb=" C ASN D 287 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.51e+00 bond pdb=" CA SER B 576 " pdb=" C SER B 576 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.31e-02 5.83e+03 3.31e+00 bond pdb=" CA ASN C 287 " pdb=" C ASN C 287 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.26e+00 bond pdb=" C TYR F 399 " pdb=" N PHE F 400 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.83e-02 1.25e+03 3.18e+00 ... (remaining 18874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 25070 2.52 - 5.03: 551 5.03 - 7.55: 55 7.55 - 10.07: 17 10.07 - 12.58: 2 Bond angle restraints: 25695 Sorted by residual: angle pdb=" N ARG A 485 " pdb=" CA ARG A 485 " pdb=" C ARG A 485 " ideal model delta sigma weight residual 110.30 122.88 -12.58 1.50e+00 4.44e-01 7.04e+01 angle pdb=" N GLY E 453 " pdb=" CA GLY E 453 " pdb=" C GLY E 453 " ideal model delta sigma weight residual 111.72 122.45 -10.73 1.31e+00 5.83e-01 6.71e+01 angle pdb=" N VAL C 493 " pdb=" CA VAL C 493 " pdb=" C VAL C 493 " ideal model delta sigma weight residual 110.62 118.17 -7.55 1.02e+00 9.61e-01 5.48e+01 angle pdb=" N MET B 436 " pdb=" CA MET B 436 " pdb=" C MET B 436 " ideal model delta sigma weight residual 110.33 119.61 -9.28 1.29e+00 6.01e-01 5.18e+01 angle pdb=" N ASN L 54 " pdb=" CA ASN L 54 " pdb=" C ASN L 54 " ideal model delta sigma weight residual 113.01 121.26 -8.25 1.20e+00 6.94e-01 4.73e+01 ... (remaining 25690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10598 17.31 - 34.62: 335 34.62 - 51.92: 68 51.92 - 69.23: 21 69.23 - 86.54: 17 Dihedral angle restraints: 11039 sinusoidal: 4361 harmonic: 6678 Sorted by residual: dihedral pdb=" CB CYS L 45 " pdb=" SG CYS L 45 " pdb=" SG CYS L 110 " pdb=" CB CYS L 110 " ideal model delta sinusoidal sigma weight residual 93.00 132.72 -39.72 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CA SER H 26 " pdb=" C SER H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN L 28 " pdb=" C GLN L 28 " pdb=" N SER L 29 " pdb=" CA SER L 29 " ideal model delta harmonic sigma weight residual 180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 11036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2334 0.090 - 0.180: 275 0.180 - 0.270: 37 0.270 - 0.360: 4 0.360 - 0.451: 3 Chirality restraints: 2653 Sorted by residual: chirality pdb=" CA ASN L 54 " pdb=" N ASN L 54 " pdb=" C ASN L 54 " pdb=" CB ASN L 54 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ARG A 485 " pdb=" N ARG A 485 " pdb=" C ARG A 485 " pdb=" CB ARG A 485 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA ALA L 73 " pdb=" N ALA L 73 " pdb=" C ALA L 73 " pdb=" CB ALA L 73 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2650 not shown) Planarity restraints: 3413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 359 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C ALA F 359 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA F 359 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS F 360 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 575 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C GLU B 575 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU B 575 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 576 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 125 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C GLU H 125 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU H 125 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL H 126 " 0.012 2.00e-02 2.50e+03 ... (remaining 3410 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 316 2.64 - 3.21: 16657 3.21 - 3.77: 29249 3.77 - 4.34: 43286 4.34 - 4.90: 69576 Nonbonded interactions: 159084 Sorted by model distance: nonbonded pdb=" OD1 ASN A 253 " pdb=" NE2 GLN A 376 " model vdw 2.077 3.120 nonbonded pdb=" NZ LYS D 323 " pdb=" OD1 ASN D 336 " model vdw 2.203 3.120 nonbonded pdb=" NH2 ARG D 485 " pdb=" OG SER D 576 " model vdw 2.207 3.120 nonbonded pdb=" NZ LYS F 323 " pdb=" OD1 ASN F 336 " model vdw 2.211 3.120 nonbonded pdb=" OG SER B 424 " pdb=" OD1 ASP C 626 " model vdw 2.213 3.040 ... (remaining 159079 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 241 through 685) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.006 0.055 18881 Z= 0.287 Angle : 0.901 12.582 25699 Z= 0.553 Chirality : 0.061 0.451 2653 Planarity : 0.005 0.047 3413 Dihedral : 10.449 86.540 6771 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.05 % Allowed : 2.10 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.14), residues: 2283 helix: -4.06 (0.34), residues: 107 sheet: -0.93 (0.17), residues: 612 loop : -0.81 (0.13), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG F 734 TYR 0.021 0.003 TYR E 445 PHE 0.025 0.002 PHE C 367 TRP 0.031 0.003 TRP C 228 HIS 0.013 0.002 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00569 (18879) covalent geometry : angle 0.90099 (25695) SS BOND : bond 0.00807 ( 2) SS BOND : angle 0.73492 ( 4) hydrogen bonds : bond 0.22620 ( 241) hydrogen bonds : angle 9.69533 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 402 time to evaluate : 0.643 Fit side-chains REVERT: A 412 GLN cc_start: 0.7739 (pt0) cc_final: 0.7445 (pp30) REVERT: A 531 GLU cc_start: 0.5837 (mt-10) cc_final: 0.5564 (pt0) REVERT: A 557 LYS cc_start: 0.7098 (mptt) cc_final: 0.6627 (mmmt) REVERT: A 567 LYS cc_start: 0.7609 (pttm) cc_final: 0.7304 (ptpp) REVERT: A 574 THR cc_start: 0.8264 (p) cc_final: 0.7896 (p) REVERT: A 575 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 238 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7162 (ptp-170) REVERT: C 312 ARG cc_start: 0.7542 (mtt90) cc_final: 0.7307 (mtp180) REVERT: C 343 GLN cc_start: 0.6489 (mt0) cc_final: 0.6200 (mt0) REVERT: C 406 ARG cc_start: 0.6416 (mtt180) cc_final: 0.5689 (mtm110) REVERT: C 641 LYS cc_start: 0.8251 (mtmt) cc_final: 0.8047 (mttm) REVERT: C 736 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8181 (tp) REVERT: D 254 ASN cc_start: 0.7054 (m-40) cc_final: 0.6592 (t0) REVERT: D 419 ASN cc_start: 0.8079 (t0) cc_final: 0.7231 (m110) REVERT: D 641 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7626 (mttp) REVERT: E 449 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8442 (ttmt) REVERT: E 514 ARG cc_start: 0.7018 (mtm180) cc_final: 0.5464 (mmm160) REVERT: F 387 GLN cc_start: 0.6714 (mt0) cc_final: 0.6190 (tp40) REVERT: F 403 GLN cc_start: 0.7033 (tt0) cc_final: 0.6686 (mm-40) REVERT: F 449 LYS cc_start: 0.7952 (mttt) cc_final: 0.7696 (tttt) REVERT: F 488 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8494 (ptt90) REVERT: H 50 ASN cc_start: 0.9160 (m-40) cc_final: 0.8895 (m-40) REVERT: H 103 ASN cc_start: 0.7867 (p0) cc_final: 0.7566 (p0) outliers start: 21 outliers final: 8 residues processed: 417 average time/residue: 0.1615 time to fit residues: 99.4682 Evaluate side-chains 243 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 233 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 624 HIS A 646 GLN A 651 ASN A 673 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN C 254 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN C 452 ASN C 458 GLN C 497 ASN C 498 ASN C 515 ASN C 608 GLN C 646 GLN C 673 GLN C 700 GLN C 704 ASN D 253 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN D 646 GLN D 651 ASN ** D 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 608 GLN F 229 HIS ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN F 343 GLN F 430 GLN F 497 ASN F 584 HIS F 608 GLN F 624 HIS F 646 GLN F 651 ASN F 673 GLN ** L 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100485 restraints weight = 26340.484| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.44 r_work: 0.2994 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18881 Z= 0.167 Angle : 0.608 8.907 25699 Z= 0.322 Chirality : 0.045 0.176 2653 Planarity : 0.005 0.042 3413 Dihedral : 6.168 58.360 2530 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.95 % Allowed : 6.39 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.15), residues: 2283 helix: -3.52 (0.41), residues: 98 sheet: -0.78 (0.18), residues: 584 loop : -0.49 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 106 TYR 0.017 0.002 TYR A 277 PHE 0.015 0.002 PHE C 367 TRP 0.017 0.002 TRP C 228 HIS 0.009 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00389 (18879) covalent geometry : angle 0.60783 (25695) SS BOND : bond 0.00711 ( 2) SS BOND : angle 0.74810 ( 4) hydrogen bonds : bond 0.04292 ( 241) hydrogen bonds : angle 7.01931 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.834 Fit side-chains REVERT: A 312 ARG cc_start: 0.7463 (mtt90) cc_final: 0.7229 (mtt180) REVERT: A 412 GLN cc_start: 0.8011 (pt0) cc_final: 0.7524 (pp30) REVERT: A 531 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5787 (pt0) REVERT: A 567 LYS cc_start: 0.7618 (pttm) cc_final: 0.7271 (ptpp) REVERT: A 574 THR cc_start: 0.8495 (p) cc_final: 0.8258 (m) REVERT: C 238 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7347 (ptm160) REVERT: C 312 ARG cc_start: 0.7423 (mtt90) cc_final: 0.7220 (mtp180) REVERT: C 343 GLN cc_start: 0.6603 (mt0) cc_final: 0.6333 (mt0) REVERT: C 406 ARG cc_start: 0.6571 (mtt180) cc_final: 0.5704 (mtm110) REVERT: D 254 ASN cc_start: 0.7469 (m-40) cc_final: 0.7048 (t0) REVERT: D 416 GLU cc_start: 0.7575 (tp30) cc_final: 0.7264 (mp0) REVERT: D 641 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7581 (mttp) REVERT: E 449 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8564 (ttmt) REVERT: E 514 ARG cc_start: 0.6888 (mtm180) cc_final: 0.5250 (mmm160) REVERT: F 387 GLN cc_start: 0.6917 (mt0) cc_final: 0.6084 (tp40) REVERT: F 403 GLN cc_start: 0.7282 (tt0) cc_final: 0.6867 (mm-40) REVERT: F 488 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8356 (ptt90) outliers start: 39 outliers final: 30 residues processed: 282 average time/residue: 0.1556 time to fit residues: 66.2020 Evaluate side-chains 263 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 646 GLN Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 196 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 chunk 219 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 292 HIS A 319 ASN A 673 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 628 ASN C 704 ASN D 262 ASN D 673 GLN E 497 ASN E 579 GLN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN F 651 ASN ** L 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 ASN H 22 GLN H 50 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.099129 restraints weight = 26643.879| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.44 r_work: 0.2969 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18881 Z= 0.173 Angle : 0.574 8.641 25699 Z= 0.301 Chirality : 0.044 0.186 2653 Planarity : 0.004 0.042 3413 Dihedral : 5.984 55.262 2526 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.45 % Allowed : 7.64 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2283 helix: -3.29 (0.46), residues: 86 sheet: -0.68 (0.18), residues: 601 loop : -0.32 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 550 TYR 0.017 0.002 TYR A 277 PHE 0.013 0.002 PHE C 535 TRP 0.015 0.002 TRP D 509 HIS 0.010 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00409 (18879) covalent geometry : angle 0.57355 (25695) SS BOND : bond 0.01335 ( 2) SS BOND : angle 0.88185 ( 4) hydrogen bonds : bond 0.03349 ( 241) hydrogen bonds : angle 6.52216 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.503 Fit side-chains REVERT: A 312 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7275 (mtt180) REVERT: A 412 GLN cc_start: 0.8090 (pt0) cc_final: 0.7558 (pp30) REVERT: A 531 GLU cc_start: 0.6422 (mt-10) cc_final: 0.5993 (pt0) REVERT: A 567 LYS cc_start: 0.7679 (pttm) cc_final: 0.7341 (ptpp) REVERT: C 238 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7442 (mtp180) REVERT: C 312 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7230 (mtp180) REVERT: C 343 GLN cc_start: 0.6619 (mt0) cc_final: 0.6369 (mt0) REVERT: C 458 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7471 (mm110) REVERT: C 579 GLN cc_start: 0.8153 (mt0) cc_final: 0.7914 (mt0) REVERT: D 254 ASN cc_start: 0.7414 (m-40) cc_final: 0.7018 (t0) REVERT: D 414 SER cc_start: 0.8486 (p) cc_final: 0.8273 (t) REVERT: D 416 GLU cc_start: 0.7623 (tp30) cc_final: 0.7284 (mp0) REVERT: E 514 ARG cc_start: 0.6862 (mtm180) cc_final: 0.5194 (mmm160) REVERT: F 387 GLN cc_start: 0.6921 (mt0) cc_final: 0.6056 (tp40) REVERT: F 403 GLN cc_start: 0.7280 (tt0) cc_final: 0.6830 (mm-40) REVERT: F 449 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7668 (ttmm) REVERT: F 488 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8717 (ptt180) outliers start: 49 outliers final: 39 residues processed: 273 average time/residue: 0.1410 time to fit residues: 58.5436 Evaluate side-chains 264 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 90 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 156 optimal weight: 0.2980 chunk 175 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN F 290 HIS ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 646 GLN L 28 GLN L 54 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 = 0.3314 r_free = 0.3314 target = 0.117609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097913 restraints weight = 26740.340| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.45 r_work: 0.2971 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18881 Z= 0.201 Angle : 0.584 8.467 25699 Z= 0.306 Chirality : 0.044 0.175 2653 Planarity : 0.005 0.039 3413 Dihedral : 5.848 52.680 2523 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.80 % Allowed : 8.09 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.16), residues: 2283 helix: -3.31 (0.46), residues: 80 sheet: -0.59 (0.19), residues: 569 loop : -0.35 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 550 TYR 0.018 0.002 TYR A 277 PHE 0.014 0.002 PHE C 535 TRP 0.016 0.002 TRP D 509 HIS 0.011 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00477 (18879) covalent geometry : angle 0.58405 (25695) SS BOND : bond 0.00917 ( 2) SS BOND : angle 0.73315 ( 4) hydrogen bonds : bond 0.03272 ( 241) hydrogen bonds : angle 6.41626 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 312 ARG cc_start: 0.7535 (mtt90) cc_final: 0.7311 (mtt180) REVERT: A 412 GLN cc_start: 0.8130 (pt0) cc_final: 0.7569 (pp30) REVERT: A 531 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6038 (pt0) REVERT: A 567 LYS cc_start: 0.7702 (pttm) cc_final: 0.7376 (ptpp) REVERT: C 238 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7455 (mtp180) REVERT: C 312 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7242 (mtp180) REVERT: C 343 GLN cc_start: 0.6672 (mt0) cc_final: 0.6391 (mt0) REVERT: C 458 GLN cc_start: 0.7991 (mm110) cc_final: 0.7732 (mm-40) REVERT: C 550 ARG cc_start: 0.8312 (ttt-90) cc_final: 0.7909 (ttt-90) REVERT: C 718 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 254 ASN cc_start: 0.7460 (m-40) cc_final: 0.7087 (t0) REVERT: D 414 SER cc_start: 0.8479 (p) cc_final: 0.8268 (t) REVERT: E 514 ARG cc_start: 0.6854 (mtm180) cc_final: 0.5265 (mmm160) REVERT: F 387 GLN cc_start: 0.6977 (mt0) cc_final: 0.6058 (tp40) REVERT: F 403 GLN cc_start: 0.7346 (tt0) cc_final: 0.6859 (mm-40) REVERT: F 449 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7633 (ttmm) REVERT: F 488 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8744 (ptt180) outliers start: 56 outliers final: 46 residues processed: 267 average time/residue: 0.1539 time to fit residues: 62.2018 Evaluate side-chains 267 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 646 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 107 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS C 704 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 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 = 0.3295 r_free = 0.3295 target = 0.116140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096500 restraints weight = 26650.751| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.44 r_work: 0.2932 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18881 Z= 0.245 Angle : 0.616 8.559 25699 Z= 0.324 Chirality : 0.046 0.182 2653 Planarity : 0.005 0.045 3413 Dihedral : 5.758 51.590 2516 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.10 % Allowed : 9.04 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.16), residues: 2283 helix: -3.40 (0.42), residues: 86 sheet: -0.65 (0.20), residues: 532 loop : -0.46 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 550 TYR 0.023 0.002 TYR F 674 PHE 0.016 0.002 PHE C 535 TRP 0.018 0.002 TRP D 509 HIS 0.012 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00585 (18879) covalent geometry : angle 0.61634 (25695) SS BOND : bond 0.01040 ( 2) SS BOND : angle 0.78875 ( 4) hydrogen bonds : bond 0.03417 ( 241) hydrogen bonds : angle 6.51533 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 0.789 Fit side-chains REVERT: A 312 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7322 (mtt180) REVERT: A 412 GLN cc_start: 0.8164 (pt0) cc_final: 0.7549 (pp30) REVERT: A 531 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6112 (pt0) REVERT: A 567 LYS cc_start: 0.7734 (pttm) cc_final: 0.7362 (ptpp) REVERT: C 238 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7444 (mtp180) REVERT: C 312 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7266 (mtp180) REVERT: C 343 GLN cc_start: 0.6691 (mt0) cc_final: 0.6445 (mt0) REVERT: C 406 ARG cc_start: 0.6615 (mtt180) cc_final: 0.5410 (mtm110) REVERT: C 550 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7864 (ttt-90) REVERT: C 718 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 254 ASN cc_start: 0.7547 (m-40) cc_final: 0.7170 (t0) REVERT: E 485 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6117 (ttm170) REVERT: E 514 ARG cc_start: 0.6858 (mtm180) cc_final: 0.5079 (ptt180) REVERT: E 531 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6937 (mt-10) REVERT: F 387 GLN cc_start: 0.6983 (mt0) cc_final: 0.6385 (mm-40) REVERT: F 403 GLN cc_start: 0.7356 (tt0) cc_final: 0.6822 (mm-40) REVERT: F 449 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7634 (ttmm) REVERT: F 488 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (ptt180) outliers start: 62 outliers final: 52 residues processed: 263 average time/residue: 0.1538 time to fit residues: 61.2532 Evaluate side-chains 269 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 122 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN D 624 HIS ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN H 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.097652 restraints weight = 26405.334| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.45 r_work: 0.2951 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18881 Z= 0.179 Angle : 0.554 8.045 25699 Z= 0.290 Chirality : 0.043 0.160 2653 Planarity : 0.004 0.040 3413 Dihedral : 5.425 51.885 2516 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.85 % Allowed : 9.69 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.16), residues: 2283 helix: -3.35 (0.43), residues: 86 sheet: -0.56 (0.20), residues: 542 loop : -0.40 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 406 TYR 0.019 0.002 TYR F 674 PHE 0.013 0.002 PHE C 535 TRP 0.015 0.002 TRP D 509 HIS 0.009 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00423 (18879) covalent geometry : angle 0.55386 (25695) SS BOND : bond 0.00852 ( 2) SS BOND : angle 0.73200 ( 4) hydrogen bonds : bond 0.03044 ( 241) hydrogen bonds : angle 6.28467 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 312 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7347 (mtt180) REVERT: A 412 GLN cc_start: 0.8207 (pt0) cc_final: 0.7552 (pp30) REVERT: A 531 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6159 (pt0) REVERT: A 567 LYS cc_start: 0.7704 (pttm) cc_final: 0.7349 (ptpp) REVERT: C 238 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7447 (mtp180) REVERT: C 312 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7222 (mtp180) REVERT: C 343 GLN cc_start: 0.6676 (mt0) cc_final: 0.6434 (mt0) REVERT: C 550 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.7860 (ttt-90) REVERT: C 718 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 254 ASN cc_start: 0.7549 (m-40) cc_final: 0.7171 (t0) REVERT: D 284 PHE cc_start: 0.7573 (m-80) cc_final: 0.7262 (m-10) REVERT: E 514 ARG cc_start: 0.6832 (mtm180) cc_final: 0.5699 (mtp180) REVERT: F 387 GLN cc_start: 0.6983 (mt0) cc_final: 0.6411 (mm-40) REVERT: F 403 GLN cc_start: 0.7399 (tt0) cc_final: 0.6860 (mm-40) REVERT: F 449 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7616 (ttmm) REVERT: F 488 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8769 (ttp-170) outliers start: 57 outliers final: 54 residues processed: 261 average time/residue: 0.1545 time to fit residues: 61.1037 Evaluate side-chains 270 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 238 ARG Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 198 optimal weight: 0.3980 chunk 26 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN H 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.096674 restraints weight = 26800.504| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.45 r_work: 0.2935 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18881 Z= 0.234 Angle : 0.600 8.222 25699 Z= 0.315 Chirality : 0.045 0.162 2653 Planarity : 0.005 0.041 3413 Dihedral : 5.578 52.130 2515 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.05 % Allowed : 10.04 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.16), residues: 2283 helix: -3.47 (0.42), residues: 86 sheet: -0.63 (0.20), residues: 532 loop : -0.49 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 406 TYR 0.031 0.002 TYR F 674 PHE 0.016 0.002 PHE C 535 TRP 0.018 0.002 TRP D 509 HIS 0.011 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00557 (18879) covalent geometry : angle 0.59966 (25695) SS BOND : bond 0.01024 ( 2) SS BOND : angle 0.77750 ( 4) hydrogen bonds : bond 0.03306 ( 241) hydrogen bonds : angle 6.42881 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.673 Fit side-chains REVERT: A 312 ARG cc_start: 0.7557 (mtt90) cc_final: 0.7343 (mtt180) REVERT: A 531 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6105 (pt0) REVERT: A 567 LYS cc_start: 0.7725 (pttm) cc_final: 0.7358 (ptpp) REVERT: C 238 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7470 (mtp180) REVERT: C 312 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7236 (mtp180) REVERT: C 343 GLN cc_start: 0.6697 (mt0) cc_final: 0.6461 (mt0) REVERT: C 406 ARG cc_start: 0.6662 (mtt180) cc_final: 0.5422 (mtm110) REVERT: C 550 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.7828 (ttt-90) REVERT: C 718 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 254 ASN cc_start: 0.7475 (m-40) cc_final: 0.7101 (t0) REVERT: D 284 PHE cc_start: 0.7589 (m-80) cc_final: 0.7258 (m-10) REVERT: E 485 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6049 (ttm170) REVERT: E 514 ARG cc_start: 0.6843 (mtm180) cc_final: 0.5086 (ptt180) REVERT: E 531 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6902 (mt-10) REVERT: F 373 MET cc_start: 0.8344 (ttt) cc_final: 0.8075 (ttp) REVERT: F 387 GLN cc_start: 0.6997 (mt0) cc_final: 0.6380 (mm-40) REVERT: F 403 GLN cc_start: 0.7405 (tt0) cc_final: 0.6833 (mm-40) REVERT: F 449 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7627 (ttmm) REVERT: F 488 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8665 (ptt180) outliers start: 61 outliers final: 55 residues processed: 259 average time/residue: 0.1526 time to fit residues: 60.0662 Evaluate side-chains 270 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 101 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN F 336 ASN F 646 GLN F 651 ASN L 54 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 = 0.3312 r_free = 0.3312 target = 0.117369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097937 restraints weight = 26526.426| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.45 r_work: 0.2938 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18881 Z= 0.191 Angle : 0.566 7.854 25699 Z= 0.297 Chirality : 0.043 0.161 2653 Planarity : 0.005 0.039 3413 Dihedral : 5.459 51.928 2515 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.95 % Allowed : 10.19 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.16), residues: 2283 helix: -3.45 (0.43), residues: 86 sheet: -0.60 (0.21), residues: 532 loop : -0.45 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 406 TYR 0.029 0.002 TYR F 674 PHE 0.014 0.002 PHE C 535 TRP 0.016 0.002 TRP D 509 HIS 0.009 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00451 (18879) covalent geometry : angle 0.56593 (25695) SS BOND : bond 0.00907 ( 2) SS BOND : angle 0.74946 ( 4) hydrogen bonds : bond 0.03113 ( 241) hydrogen bonds : angle 6.33227 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 312 ARG cc_start: 0.7552 (mtt90) cc_final: 0.7339 (mtt180) REVERT: A 531 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6150 (pt0) REVERT: A 567 LYS cc_start: 0.7741 (pttm) cc_final: 0.7372 (ptpp) REVERT: C 238 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7537 (mtp180) REVERT: C 312 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7242 (mtp180) REVERT: C 343 GLN cc_start: 0.6669 (mt0) cc_final: 0.6424 (mt0) REVERT: C 550 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.7840 (ttt-90) REVERT: C 718 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 254 ASN cc_start: 0.7457 (m-40) cc_final: 0.7087 (t0) REVERT: D 284 PHE cc_start: 0.7643 (m-80) cc_final: 0.7332 (m-10) REVERT: E 514 ARG cc_start: 0.6847 (mtm180) cc_final: 0.5071 (ptt180) REVERT: F 373 MET cc_start: 0.8308 (ttt) cc_final: 0.8084 (ttp) REVERT: F 387 GLN cc_start: 0.6995 (mt0) cc_final: 0.6378 (mm-40) REVERT: F 403 GLN cc_start: 0.7443 (tt0) cc_final: 0.6861 (mm-40) REVERT: F 449 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7605 (ttmm) REVERT: F 488 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8750 (ttp-170) outliers start: 59 outliers final: 57 residues processed: 259 average time/residue: 0.1541 time to fit residues: 60.4006 Evaluate side-chains 272 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 646 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 206 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN F 336 ASN F 646 GLN F 651 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 = 0.3306 r_free = 0.3306 target = 0.116959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097374 restraints weight = 26494.341| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.45 r_work: 0.2943 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18881 Z= 0.160 Angle : 0.541 7.644 25699 Z= 0.283 Chirality : 0.043 0.159 2653 Planarity : 0.004 0.040 3413 Dihedral : 5.304 51.738 2515 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.65 % Allowed : 10.79 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2283 helix: -3.36 (0.44), residues: 86 sheet: -0.57 (0.21), residues: 532 loop : -0.40 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 550 TYR 0.027 0.002 TYR F 674 PHE 0.013 0.002 PHE C 535 TRP 0.015 0.002 TRP D 509 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00378 (18879) covalent geometry : angle 0.54107 (25695) SS BOND : bond 0.00821 ( 2) SS BOND : angle 0.71873 ( 4) hydrogen bonds : bond 0.02943 ( 241) hydrogen bonds : angle 6.23042 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 312 ARG cc_start: 0.7559 (mtt90) cc_final: 0.7352 (mtt180) REVERT: A 531 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6189 (pt0) REVERT: A 567 LYS cc_start: 0.7706 (pttm) cc_final: 0.7351 (ptpp) REVERT: B 454 SER cc_start: 0.8141 (t) cc_final: 0.7909 (p) REVERT: C 238 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7533 (mtp180) REVERT: C 312 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7248 (mtp180) REVERT: C 343 GLN cc_start: 0.6654 (mt0) cc_final: 0.6406 (mt0) REVERT: C 550 ARG cc_start: 0.8309 (ttt-90) cc_final: 0.7831 (ttt-90) REVERT: C 718 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D 254 ASN cc_start: 0.7457 (m-40) cc_final: 0.7086 (t0) REVERT: D 284 PHE cc_start: 0.7612 (m-80) cc_final: 0.7363 (m-10) REVERT: E 514 ARG cc_start: 0.6806 (mtm180) cc_final: 0.5681 (mtp180) REVERT: F 373 MET cc_start: 0.8293 (ttt) cc_final: 0.8075 (ttp) REVERT: F 387 GLN cc_start: 0.7082 (mt0) cc_final: 0.6433 (mm-40) REVERT: F 403 GLN cc_start: 0.7451 (tt0) cc_final: 0.6869 (mm-40) REVERT: F 449 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7593 (ttmm) REVERT: F 488 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8694 (ttp-170) REVERT: L 64 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7763 (mttp) outliers start: 53 outliers final: 51 residues processed: 255 average time/residue: 0.1577 time to fit residues: 60.5417 Evaluate side-chains 267 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 646 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN F 336 ASN F 343 GLN F 651 ASN L 54 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 = 0.3321 r_free = 0.3321 target = 0.117989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098558 restraints weight = 26442.552| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.46 r_work: 0.2944 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18881 Z= 0.162 Angle : 0.541 7.630 25699 Z= 0.283 Chirality : 0.043 0.160 2653 Planarity : 0.004 0.039 3413 Dihedral : 5.261 51.365 2515 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.65 % Allowed : 10.84 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.17), residues: 2283 helix: -3.35 (0.44), residues: 86 sheet: -0.53 (0.21), residues: 532 loop : -0.40 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 142 TYR 0.026 0.002 TYR F 674 PHE 0.013 0.002 PHE C 535 TRP 0.015 0.002 TRP D 509 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00383 (18879) covalent geometry : angle 0.54060 (25695) SS BOND : bond 0.00827 ( 2) SS BOND : angle 0.71114 ( 4) hydrogen bonds : bond 0.02934 ( 241) hydrogen bonds : angle 6.20333 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.7564 (mtt90) cc_final: 0.7359 (mtt180) REVERT: A 531 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6181 (pt0) REVERT: A 567 LYS cc_start: 0.7709 (pttm) cc_final: 0.7356 (ptpp) REVERT: B 454 SER cc_start: 0.8159 (t) cc_final: 0.7872 (p) REVERT: C 233 GLN cc_start: 0.8652 (mt0) cc_final: 0.7951 (mm-40) REVERT: C 238 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7543 (mtp180) REVERT: C 312 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7253 (mtp180) REVERT: C 317 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 343 GLN cc_start: 0.6653 (mt0) cc_final: 0.6404 (mt0) REVERT: C 550 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7821 (ttt-90) REVERT: C 718 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7750 (mt-10) REVERT: D 254 ASN cc_start: 0.7439 (m-40) cc_final: 0.7085 (t0) REVERT: D 284 PHE cc_start: 0.7594 (m-80) cc_final: 0.7351 (m-10) REVERT: E 514 ARG cc_start: 0.6754 (mtm180) cc_final: 0.5678 (mtp180) REVERT: F 373 MET cc_start: 0.8291 (ttt) cc_final: 0.8074 (ttp) REVERT: F 387 GLN cc_start: 0.7078 (mt0) cc_final: 0.6426 (mm-40) REVERT: F 403 GLN cc_start: 0.7461 (tt0) cc_final: 0.6879 (mm-40) REVERT: F 449 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7594 (ttmm) REVERT: F 488 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7313 (ptp-170) REVERT: L 64 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7765 (mttp) outliers start: 53 outliers final: 50 residues processed: 253 average time/residue: 0.1546 time to fit residues: 59.1269 Evaluate side-chains 269 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain F residue 711 VAL Chi-restraints excluded: chain F residue 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 148 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 128 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 HIS ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN F 646 GLN F 651 ASN L 54 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 = 0.3298 r_free = 0.3298 target = 0.116372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.096985 restraints weight = 26626.231| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.45 r_work: 0.2919 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18881 Z= 0.263 Angle : 0.620 8.143 25699 Z= 0.325 Chirality : 0.046 0.167 2653 Planarity : 0.005 0.042 3413 Dihedral : 5.636 51.774 2515 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.80 % Allowed : 10.74 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.16), residues: 2283 helix: -3.54 (0.41), residues: 86 sheet: -0.65 (0.21), residues: 532 loop : -0.55 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 142 TYR 0.027 0.002 TYR F 674 PHE 0.017 0.002 PHE D 629 TRP 0.018 0.002 TRP D 509 HIS 0.012 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00625 (18879) covalent geometry : angle 0.61982 (25695) SS BOND : bond 0.01095 ( 2) SS BOND : angle 0.74656 ( 4) hydrogen bonds : bond 0.03466 ( 241) hydrogen bonds : angle 6.49498 ( 495) =============================================================================== Job complete usr+sys time: 4863.42 seconds wall clock time: 84 minutes 24.10 seconds (5064.10 seconds total)