Starting phenix.real_space_refine on Sun Jun 15 22:07:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7n_44317/06_2025/9b7n_44317.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7n_44317/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7n_44317/06_2025/9b7n_44317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7n_44317/06_2025/9b7n_44317.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7n_44317/06_2025/9b7n_44317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7n_44317/06_2025/9b7n_44317.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.80, per 1000 atoms: 0.59 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: 4.32 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.13 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: 5.42 Time building geometry restraints manager: 5.16 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 41.890 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.003 TRP C 228 HIS 0.013 0.002 HIS A 290 PHE 0.025 0.002 PHE C 367 TYR 0.021 0.003 TYR E 445 ARG 0.016 0.002 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.22620 ( 241) hydrogen bonds : angle 9.69533 ( 495) SS BOND : bond 0.00807 ( 2) SS BOND : angle 0.73492 ( 4) covalent geometry : bond 0.00569 (18879) covalent geometry : angle 0.90099 (25695) *********************** 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 : 2.045 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: 0.3580 time to fit residues: 220.6863 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 : 2.352 ------------------------------------------------------------------------------- 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 192 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 403 GLN 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100285 restraints weight = 26353.699| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.43 r_work: 0.2989 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18881 Z= 0.176 Angle : 0.614 8.851 25699 Z= 0.326 Chirality : 0.045 0.168 2653 Planarity : 0.005 0.042 3413 Dihedral : 6.212 58.060 2530 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.05 % Allowed : 6.49 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2283 helix: -3.52 (0.41), residues: 98 sheet: -0.76 (0.19), residues: 563 loop : -0.50 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 228 HIS 0.010 0.002 HIS A 290 PHE 0.016 0.002 PHE C 367 TYR 0.018 0.002 TYR C 257 ARG 0.007 0.001 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 241) hydrogen bonds : angle 6.95843 ( 495) SS BOND : bond 0.00720 ( 2) SS BOND : angle 0.77401 ( 4) covalent geometry : bond 0.00408 (18879) covalent geometry : angle 0.61409 (25695) *********************** 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 302 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 1.945 Fit side-chains REVERT: A 312 ARG cc_start: 0.7469 (mtt90) cc_final: 0.7234 (mtt180) REVERT: A 412 GLN cc_start: 0.8012 (pt0) cc_final: 0.7529 (pp30) REVERT: A 531 GLU cc_start: 0.6224 (mt-10) cc_final: 0.5847 (pt0) REVERT: A 567 LYS cc_start: 0.7637 (pttm) cc_final: 0.7286 (ptpp) REVERT: C 238 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7501 (mtp180) REVERT: C 312 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7228 (mtp180) REVERT: C 343 GLN cc_start: 0.6611 (mt0) cc_final: 0.6342 (mt0) REVERT: C 406 ARG cc_start: 0.6564 (mtt180) cc_final: 0.5694 (mtm110) REVERT: D 254 ASN cc_start: 0.7467 (m-40) cc_final: 0.7053 (t0) REVERT: D 416 GLU cc_start: 0.7584 (tp30) cc_final: 0.7273 (mp0) REVERT: D 641 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7559 (mttp) REVERT: E 449 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8572 (ttmt) REVERT: E 514 ARG cc_start: 0.6869 (mtm180) cc_final: 0.5217 (mmm160) REVERT: F 387 GLN cc_start: 0.6922 (mt0) cc_final: 0.6076 (tp40) REVERT: F 403 GLN cc_start: 0.7286 (tt0) cc_final: 0.6869 (mm-40) REVERT: F 488 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8320 (ptt90) outliers start: 41 outliers final: 34 residues processed: 284 average time/residue: 0.3216 time to fit residues: 137.8214 Evaluate side-chains 267 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 640 MET 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 381 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 40 SER 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 189 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 624 HIS D 673 GLN E 497 ASN ** 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 = 0.3328 r_free = 0.3328 target = 0.118580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099262 restraints weight = 26729.576| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.43 r_work: 0.2974 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18881 Z= 0.146 Angle : 0.550 8.349 25699 Z= 0.289 Chirality : 0.043 0.176 2653 Planarity : 0.004 0.039 3413 Dihedral : 5.838 56.249 2526 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.60 % Allowed : 7.59 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2283 helix: -3.44 (0.42), residues: 98 sheet: -0.63 (0.19), residues: 581 loop : -0.30 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 228 HIS 0.009 0.001 HIS C 290 PHE 0.012 0.002 PHE A 286 TYR 0.016 0.002 TYR A 613 ARG 0.005 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 241) hydrogen bonds : angle 6.37677 ( 495) SS BOND : bond 0.00359 ( 2) SS BOND : angle 0.92479 ( 4) covalent geometry : bond 0.00344 (18879) covalent geometry : angle 0.55006 (25695) *********************** 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 305 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 1.917 Fit side-chains REVERT: A 312 ARG cc_start: 0.7517 (mtt90) cc_final: 0.7309 (mtt180) REVERT: A 412 GLN cc_start: 0.8067 (pt0) cc_final: 0.7555 (pp30) REVERT: A 531 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6038 (pt0) REVERT: A 567 LYS cc_start: 0.7689 (pttm) cc_final: 0.7354 (ptpp) REVERT: C 238 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7446 (mtp180) REVERT: C 312 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7248 (mtp180) REVERT: C 343 GLN cc_start: 0.6604 (mt0) cc_final: 0.6369 (mt0) REVERT: C 431 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8688 (t) REVERT: C 458 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7416 (mm110) REVERT: C 550 ARG cc_start: 0.8285 (ttt-90) cc_final: 0.8050 (ttt-90) REVERT: C 579 GLN cc_start: 0.8131 (mt0) cc_final: 0.7914 (mt0) REVERT: D 254 ASN cc_start: 0.7452 (m-40) cc_final: 0.7064 (t0) REVERT: D 416 GLU cc_start: 0.7588 (tp30) cc_final: 0.7242 (mp0) REVERT: E 514 ARG cc_start: 0.6858 (mtm180) cc_final: 0.5221 (mmm160) REVERT: F 387 GLN cc_start: 0.6956 (mt0) cc_final: 0.6106 (tp40) REVERT: F 403 GLN cc_start: 0.7268 (tt0) cc_final: 0.6869 (mm-40) REVERT: F 449 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7670 (ttmm) REVERT: F 488 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (ptt180) REVERT: F 709 ASN cc_start: 0.8915 (m-40) cc_final: 0.8712 (m-40) outliers start: 52 outliers final: 40 residues processed: 280 average time/residue: 0.3102 time to fit residues: 132.1036 Evaluate side-chains 270 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR 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 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 381 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 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 588 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 76 LEU Chi-restraints excluded: chain L residue 96 THR 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 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 112 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN E 579 GLN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 336 ASN L 28 GLN L 54 ASN H 22 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098322 restraints weight = 26512.460| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.44 r_work: 0.2956 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18881 Z= 0.192 Angle : 0.576 8.387 25699 Z= 0.301 Chirality : 0.044 0.169 2653 Planarity : 0.005 0.039 3413 Dihedral : 5.760 51.363 2523 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.65 % Allowed : 8.49 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2283 helix: -3.25 (0.47), residues: 80 sheet: -0.57 (0.19), residues: 569 loop : -0.29 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 509 HIS 0.011 0.001 HIS A 290 PHE 0.017 0.002 PHE D 284 TYR 0.017 0.002 TYR A 277 ARG 0.005 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 241) hydrogen bonds : angle 6.35743 ( 495) SS BOND : bond 0.01007 ( 2) SS BOND : angle 0.84906 ( 4) covalent geometry : bond 0.00457 (18879) covalent geometry : angle 0.57596 (25695) *********************** 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: 53 poor density : 236 time to evaluate : 2.084 Fit side-chains REVERT: A 312 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7298 (mtt180) REVERT: A 412 GLN cc_start: 0.8132 (pt0) cc_final: 0.7581 (pp30) REVERT: A 531 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6028 (pt0) REVERT: A 567 LYS cc_start: 0.7708 (pttm) cc_final: 0.7342 (ptpp) REVERT: C 238 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7453 (mtp180) REVERT: C 312 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7232 (mtp180) REVERT: C 343 GLN cc_start: 0.6668 (mt0) cc_final: 0.6385 (mt0) REVERT: C 458 GLN cc_start: 0.7934 (mm110) cc_final: 0.7702 (mm-40) REVERT: C 550 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.8048 (ttt-90) REVERT: C 718 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 254 ASN cc_start: 0.7470 (m-40) cc_final: 0.7079 (t0) REVERT: D 284 PHE cc_start: 0.7467 (m-80) cc_final: 0.7092 (m-10) REVERT: E 485 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.5697 (ttm170) REVERT: E 514 ARG cc_start: 0.6868 (mtm180) cc_final: 0.5239 (mmm160) REVERT: F 387 GLN cc_start: 0.6976 (mt0) cc_final: 0.6054 (tp40) REVERT: F 403 GLN cc_start: 0.7317 (tt0) cc_final: 0.6836 (mm-40) REVERT: F 449 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7650 (ttmm) REVERT: F 488 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8743 (ptt180) REVERT: F 514 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: F 711 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8683 (m) outliers start: 53 outliers final: 41 residues processed: 268 average time/residue: 0.3182 time to fit residues: 129.3118 Evaluate side-chains 263 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 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 381 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 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 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 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 83 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 193 optimal weight: 9.9990 chunk 144 optimal weight: 0.0070 chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 133 optimal weight: 0.0570 overall best weight: 2.0238 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN C 704 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN 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 = 0.3335 r_free = 0.3335 target = 0.119067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099768 restraints weight = 26922.766| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.45 r_work: 0.2997 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18881 Z= 0.103 Angle : 0.496 7.648 25699 Z= 0.258 Chirality : 0.041 0.161 2653 Planarity : 0.004 0.039 3413 Dihedral : 5.033 50.561 2516 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.15 % Allowed : 9.19 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2283 helix: -3.25 (0.46), residues: 86 sheet: -0.48 (0.20), residues: 575 loop : -0.14 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.005 0.001 HIS A 290 PHE 0.012 0.001 PHE D 284 TYR 0.029 0.001 TYR F 674 ARG 0.004 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02610 ( 241) hydrogen bonds : angle 5.94645 ( 495) SS BOND : bond 0.00652 ( 2) SS BOND : angle 0.74068 ( 4) covalent geometry : bond 0.00239 (18879) covalent geometry : angle 0.49552 (25695) *********************** 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 293 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8092 (pt0) cc_final: 0.7516 (pp30) REVERT: A 524 MET cc_start: 0.8163 (mtm) cc_final: 0.7820 (mtm) REVERT: A 531 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6174 (pt0) REVERT: A 567 LYS cc_start: 0.7713 (pttm) cc_final: 0.7333 (ptpp) REVERT: C 233 GLN cc_start: 0.8608 (mt0) cc_final: 0.7957 (mm-40) REVERT: C 238 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7460 (mtp180) REVERT: C 312 ARG cc_start: 0.7381 (mtt90) cc_final: 0.7179 (mtp180) REVERT: C 343 GLN cc_start: 0.6567 (mt0) cc_final: 0.6320 (mt0) REVERT: C 431 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8685 (t) REVERT: C 550 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7887 (ttt-90) REVERT: C 718 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7661 (mt-10) REVERT: D 254 ASN cc_start: 0.7459 (m-40) cc_final: 0.7075 (t0) REVERT: D 284 PHE cc_start: 0.7386 (m-80) cc_final: 0.7109 (m-10) REVERT: D 416 GLU cc_start: 0.7541 (tp30) cc_final: 0.7214 (mp0) REVERT: E 514 ARG cc_start: 0.6784 (mtm180) cc_final: 0.5161 (mmm160) REVERT: F 387 GLN cc_start: 0.6947 (mt0) cc_final: 0.6386 (mm-40) REVERT: F 403 GLN cc_start: 0.7265 (tt0) cc_final: 0.6845 (mm-40) REVERT: F 449 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7668 (ttmm) REVERT: F 456 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7453 (mm110) REVERT: F 488 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7124 (ptp-170) REVERT: F 729 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8745 (p) outliers start: 43 outliers final: 33 residues processed: 277 average time/residue: 0.3167 time to fit residues: 131.3007 Evaluate side-chains 268 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 561 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 673 GLN Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 238 ARG 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 729 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain H residue 31 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 40 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 124 optimal weight: 0.0070 chunk 6 optimal weight: 9.9990 overall best weight: 3.8604 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN C 704 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099056 restraints weight = 26543.894| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.45 r_work: 0.2961 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18881 Z= 0.150 Angle : 0.525 7.691 25699 Z= 0.273 Chirality : 0.042 0.148 2653 Planarity : 0.004 0.038 3413 Dihedral : 5.135 51.590 2516 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.45 % Allowed : 9.14 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2283 helix: -3.17 (0.48), residues: 80 sheet: -0.37 (0.20), residues: 542 loop : -0.20 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 509 HIS 0.008 0.001 HIS A 290 PHE 0.012 0.002 PHE C 535 TYR 0.022 0.002 TYR F 674 ARG 0.003 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02854 ( 241) hydrogen bonds : angle 6.00637 ( 495) SS BOND : bond 0.00818 ( 2) SS BOND : angle 0.81737 ( 4) covalent geometry : bond 0.00354 (18879) covalent geometry : angle 0.52465 (25695) *********************** 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 283 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 2.037 Fit side-chains REVERT: A 412 GLN cc_start: 0.8166 (pt0) cc_final: 0.7542 (pp30) REVERT: A 524 MET cc_start: 0.8166 (mtm) cc_final: 0.7823 (mtm) REVERT: A 531 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6131 (pt0) REVERT: A 567 LYS cc_start: 0.7716 (pttm) cc_final: 0.7351 (ptpp) REVERT: A 615 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: C 233 GLN cc_start: 0.8649 (mt0) cc_final: 0.7958 (mm-40) REVERT: C 238 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7458 (mtp180) REVERT: C 312 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7191 (mtp180) REVERT: C 343 GLN cc_start: 0.6607 (mt0) cc_final: 0.6361 (mt0) REVERT: C 431 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8683 (t) REVERT: C 458 GLN cc_start: 0.7916 (mm110) cc_final: 0.7671 (mm-40) REVERT: C 550 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7957 (ttt-90) REVERT: C 718 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7694 (mt-10) REVERT: D 254 ASN cc_start: 0.7449 (m-40) cc_final: 0.7073 (t0) REVERT: D 284 PHE cc_start: 0.7504 (m-80) cc_final: 0.7232 (m-10) REVERT: D 416 GLU cc_start: 0.7529 (tp30) cc_final: 0.7212 (mp0) REVERT: E 485 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.5737 (ttm170) REVERT: E 514 ARG cc_start: 0.6832 (mtm180) cc_final: 0.5655 (mtp180) REVERT: F 387 GLN cc_start: 0.6945 (mt0) cc_final: 0.6369 (mm-40) REVERT: F 403 GLN cc_start: 0.7358 (tt0) cc_final: 0.6869 (mm-40) REVERT: F 449 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7645 (ttmm) REVERT: F 456 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7528 (mm110) REVERT: F 488 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7359 (ptp-170) REVERT: F 514 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7814 (mtp-110) REVERT: H 139 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7635 (mp10) outliers start: 49 outliers final: 44 residues processed: 266 average time/residue: 0.3051 time to fit residues: 122.9134 Evaluate side-chains 272 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 615 GLN 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 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 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 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 485 ARG Chi-restraints excluded: chain F residue 239 VAL 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 96 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 40 SER 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 97 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 111 optimal weight: 0.0470 chunk 29 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 40 optimal weight: 0.0970 overall best weight: 2.9680 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 336 ASN F 646 GLN F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099360 restraints weight = 26378.839| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.44 r_work: 0.2977 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18881 Z= 0.125 Angle : 0.502 7.349 25699 Z= 0.261 Chirality : 0.041 0.148 2653 Planarity : 0.004 0.037 3413 Dihedral : 5.021 51.161 2516 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.55 % Allowed : 9.44 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2283 helix: -3.15 (0.48), residues: 80 sheet: -0.35 (0.20), residues: 544 loop : -0.20 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 509 HIS 0.007 0.001 HIS A 290 PHE 0.011 0.001 PHE D 284 TYR 0.021 0.001 TYR F 674 ARG 0.003 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 241) hydrogen bonds : angle 5.90495 ( 495) SS BOND : bond 0.00756 ( 2) SS BOND : angle 0.82308 ( 4) covalent geometry : bond 0.00293 (18879) covalent geometry : angle 0.50230 (25695) *********************** 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 286 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 2.159 Fit side-chains REVERT: A 412 GLN cc_start: 0.8175 (pt0) cc_final: 0.7545 (pp30) REVERT: A 524 MET cc_start: 0.8158 (mtm) cc_final: 0.7833 (mtm) REVERT: A 531 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6166 (pt0) REVERT: A 567 LYS cc_start: 0.7730 (pttm) cc_final: 0.7368 (ptpp) REVERT: A 615 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: C 233 GLN cc_start: 0.8656 (mt0) cc_final: 0.7976 (mm-40) REVERT: C 238 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7464 (mtp180) REVERT: C 312 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7187 (mtp180) REVERT: C 343 GLN cc_start: 0.6597 (mt0) cc_final: 0.6352 (mt0) REVERT: C 550 ARG cc_start: 0.8289 (ttt-90) cc_final: 0.7980 (ttt-90) REVERT: C 718 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 254 ASN cc_start: 0.7421 (m-40) cc_final: 0.7064 (t0) REVERT: D 284 PHE cc_start: 0.7472 (m-80) cc_final: 0.7243 (m-10) REVERT: E 485 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.5692 (ttm170) REVERT: E 514 ARG cc_start: 0.6826 (mtm180) cc_final: 0.5204 (mmm160) REVERT: F 387 GLN cc_start: 0.6960 (mt0) cc_final: 0.6390 (mm-40) REVERT: F 403 GLN cc_start: 0.7343 (tt0) cc_final: 0.6873 (mm-40) REVERT: F 449 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7630 (ttmm) REVERT: F 456 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7499 (mm110) REVERT: F 488 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8590 (ttp-170) REVERT: F 514 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7845 (mtp-110) REVERT: L 25 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7393 (mm-40) REVERT: H 108 ASP cc_start: 0.7348 (p0) cc_final: 0.7116 (p0) outliers start: 51 outliers final: 44 residues processed: 268 average time/residue: 0.3140 time to fit residues: 127.9791 Evaluate side-chains 278 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 494 THR 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 E residue 485 ARG 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 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 31 VAL Chi-restraints excluded: chain H residue 40 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 101 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 135 optimal weight: 0.3980 chunk 170 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 192 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 336 ASN F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098419 restraints weight = 26389.126| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.45 r_work: 0.2954 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18881 Z= 0.173 Angle : 0.537 7.574 25699 Z= 0.280 Chirality : 0.043 0.148 2653 Planarity : 0.004 0.040 3413 Dihedral : 5.075 51.370 2515 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.50 % Allowed : 9.79 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2283 helix: -3.25 (0.47), residues: 80 sheet: -0.39 (0.21), residues: 532 loop : -0.26 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 509 HIS 0.009 0.001 HIS A 290 PHE 0.013 0.002 PHE C 535 TYR 0.019 0.002 TYR F 674 ARG 0.004 0.000 ARG F 406 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 241) hydrogen bonds : angle 6.03749 ( 495) SS BOND : bond 0.00885 ( 2) SS BOND : angle 0.88770 ( 4) covalent geometry : bond 0.00410 (18879) covalent geometry : angle 0.53655 (25695) *********************** 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 283 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8201 (pt0) cc_final: 0.7542 (pp30) REVERT: A 524 MET cc_start: 0.8170 (mtm) cc_final: 0.7842 (mtm) REVERT: A 531 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6082 (pt0) REVERT: A 567 LYS cc_start: 0.7718 (pttm) cc_final: 0.7360 (ptpp) REVERT: A 615 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: C 233 GLN cc_start: 0.8647 (mt0) cc_final: 0.7961 (mm-40) REVERT: C 238 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7525 (mtp180) REVERT: C 312 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7212 (mtp180) REVERT: C 317 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8044 (mp) REVERT: C 343 GLN cc_start: 0.6620 (mt0) cc_final: 0.6376 (mt0) REVERT: C 550 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.8011 (ttt-90) REVERT: C 718 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 254 ASN cc_start: 0.7457 (m-40) cc_final: 0.7149 (t0) REVERT: D 284 PHE cc_start: 0.7594 (m-80) cc_final: 0.7285 (m-10) REVERT: E 514 ARG cc_start: 0.6827 (mtm180) cc_final: 0.5664 (mtp180) REVERT: F 387 GLN cc_start: 0.6947 (mt0) cc_final: 0.6353 (mm-40) REVERT: F 403 GLN cc_start: 0.7324 (tt0) cc_final: 0.6825 (mm-40) REVERT: F 449 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7649 (ttmm) REVERT: F 456 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7548 (mm110) REVERT: F 488 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7401 (ptp-170) REVERT: F 514 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7903 (mtp-110) outliers start: 50 outliers final: 43 residues processed: 263 average time/residue: 0.3150 time to fit residues: 125.3935 Evaluate side-chains 273 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 491 THR 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 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 E residue 485 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 127 optimal weight: 0.2980 chunk 193 optimal weight: 7.9990 chunk 33 optimal weight: 0.0070 chunk 68 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 overall best weight: 3.0202 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 336 ASN F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.100092 restraints weight = 26474.172| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.43 r_work: 0.2970 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18881 Z= 0.126 Angle : 0.505 7.235 25699 Z= 0.262 Chirality : 0.041 0.147 2653 Planarity : 0.004 0.038 3413 Dihedral : 4.904 50.816 2515 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.50 % Allowed : 9.99 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2283 helix: -3.20 (0.48), residues: 80 sheet: -0.33 (0.21), residues: 532 loop : -0.23 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 509 HIS 0.006 0.001 HIS A 290 PHE 0.012 0.001 PHE D 284 TYR 0.029 0.001 TYR F 674 ARG 0.003 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 241) hydrogen bonds : angle 5.88076 ( 495) SS BOND : bond 0.00762 ( 2) SS BOND : angle 0.88214 ( 4) covalent geometry : bond 0.00296 (18879) covalent geometry : angle 0.50442 (25695) *********************** 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 285 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 1.903 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8189 (pt0) cc_final: 0.7516 (pp30) REVERT: A 524 MET cc_start: 0.8156 (mtm) cc_final: 0.7839 (mtm) REVERT: A 531 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6190 (pt0) REVERT: A 567 LYS cc_start: 0.7725 (pttm) cc_final: 0.7360 (ptpp) REVERT: A 615 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: C 233 GLN cc_start: 0.8611 (mt0) cc_final: 0.7949 (mm-40) REVERT: C 238 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7519 (mtp180) REVERT: C 312 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7197 (mtp180) REVERT: C 317 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8039 (mp) REVERT: C 343 GLN cc_start: 0.6600 (mt0) cc_final: 0.6358 (mt0) REVERT: C 550 ARG cc_start: 0.8257 (ttt-90) cc_final: 0.7886 (ttt-90) REVERT: C 718 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7675 (mt-10) REVERT: D 254 ASN cc_start: 0.7392 (m-40) cc_final: 0.7090 (t0) REVERT: D 284 PHE cc_start: 0.7566 (m-80) cc_final: 0.7358 (m-10) REVERT: D 416 GLU cc_start: 0.7499 (tp30) cc_final: 0.7178 (mp0) REVERT: E 485 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.5671 (ttm170) REVERT: E 514 ARG cc_start: 0.6807 (mtm180) cc_final: 0.5176 (mmm160) REVERT: E 531 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6834 (mt-10) REVERT: F 387 GLN cc_start: 0.7051 (mt0) cc_final: 0.6425 (mm-40) REVERT: F 403 GLN cc_start: 0.7316 (tt0) cc_final: 0.6842 (mm-40) REVERT: F 449 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7625 (ttmm) REVERT: F 456 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7541 (mm110) REVERT: F 488 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (ttp-170) REVERT: F 514 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7848 (mtp-110) REVERT: L 64 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7757 (mttp) outliers start: 50 outliers final: 45 residues processed: 266 average time/residue: 0.3179 time to fit residues: 128.5474 Evaluate side-chains 277 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 491 THR 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 E residue 485 ARG Chi-restraints excluded: chain F residue 238 ARG 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 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 31 VAL Chi-restraints excluded: chain H residue 40 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 336 ASN F 343 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100972 restraints weight = 26352.269| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.45 r_work: 0.2983 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18881 Z= 0.108 Angle : 0.486 7.091 25699 Z= 0.252 Chirality : 0.041 0.144 2653 Planarity : 0.004 0.038 3413 Dihedral : 4.719 49.885 2515 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 10.19 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2283 helix: -3.10 (0.49), residues: 80 sheet: -0.28 (0.21), residues: 534 loop : -0.18 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 509 HIS 0.005 0.001 HIS A 290 PHE 0.011 0.001 PHE D 284 TYR 0.027 0.001 TYR F 674 ARG 0.003 0.000 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02567 ( 241) hydrogen bonds : angle 5.70717 ( 495) SS BOND : bond 0.00703 ( 2) SS BOND : angle 0.83645 ( 4) covalent geometry : bond 0.00253 (18879) covalent geometry : angle 0.48604 (25695) ********************** 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 282 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8195 (pt0) cc_final: 0.7526 (pp30) REVERT: A 524 MET cc_start: 0.8148 (mtm) cc_final: 0.7841 (mtm) REVERT: A 531 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6267 (pt0) REVERT: A 557 LYS cc_start: 0.6608 (mptt) cc_final: 0.6385 (mttm) REVERT: A 567 LYS cc_start: 0.7750 (pttm) cc_final: 0.7386 (ptpp) REVERT: A 615 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: C 233 GLN cc_start: 0.8624 (mt0) cc_final: 0.7963 (mm-40) REVERT: C 238 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7514 (mtp180) REVERT: C 312 ARG cc_start: 0.7446 (mtt90) cc_final: 0.7195 (mtp180) REVERT: C 317 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (mp) REVERT: C 343 GLN cc_start: 0.6589 (mt0) cc_final: 0.6339 (mt0) REVERT: C 550 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.7860 (ttt-90) REVERT: C 718 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 254 ASN cc_start: 0.7456 (m-40) cc_final: 0.7127 (t0) REVERT: E 485 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.5563 (ttm170) REVERT: E 514 ARG cc_start: 0.6791 (mtm180) cc_final: 0.5163 (mmm160) REVERT: E 531 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6771 (mt-10) REVERT: F 387 GLN cc_start: 0.7069 (mt0) cc_final: 0.6452 (mm-40) REVERT: F 403 GLN cc_start: 0.7338 (tt0) cc_final: 0.6865 (mm-40) REVERT: F 449 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7627 (ttmm) REVERT: F 456 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7565 (mm110) REVERT: F 488 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7678 (ptp-170) REVERT: F 729 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8731 (p) REVERT: L 64 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7755 (mttp) outliers start: 46 outliers final: 40 residues processed: 267 average time/residue: 0.3182 time to fit residues: 128.1940 Evaluate side-chains 272 residues out of total 2002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 494 THR 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 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 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 E residue 485 ARG Chi-restraints excluded: chain F residue 238 ARG 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 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 31 VAL Chi-restraints excluded: chain H residue 40 SER 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 145 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 29 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS F 321 GLN F 336 ASN F 646 GLN F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097052 restraints weight = 26642.085| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.43 r_work: 0.2954 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18881 Z= 0.227 Angle : 0.589 7.730 25699 Z= 0.308 Chirality : 0.045 0.151 2653 Planarity : 0.005 0.040 3413 Dihedral : 5.291 50.163 2514 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.25 % Allowed : 10.34 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2283 helix: -3.26 (0.45), residues: 86 sheet: -0.40 (0.21), residues: 512 loop : -0.37 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 509 HIS 0.012 0.001 HIS A 290 PHE 0.016 0.002 PHE D 629 TYR 0.028 0.002 TYR F 674 ARG 0.007 0.001 ARG F 550 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 241) hydrogen bonds : angle 6.21364 ( 495) SS BOND : bond 0.01048 ( 2) SS BOND : angle 0.82887 ( 4) covalent geometry : bond 0.00542 (18879) covalent geometry : angle 0.58922 (25695) =============================================================================== Job complete usr+sys time: 9300.23 seconds wall clock time: 161 minutes 14.06 seconds (9674.06 seconds total)