Starting phenix.real_space_refine on Thu Feb 5 03:36:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg9_61459/02_2026/9jg9_61459.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg9_61459/02_2026/9jg9_61459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jg9_61459/02_2026/9jg9_61459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg9_61459/02_2026/9jg9_61459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jg9_61459/02_2026/9jg9_61459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg9_61459/02_2026/9jg9_61459.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.169 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 89 5.16 5 C 9085 2.51 5 N 2475 2.21 5 O 2856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14506 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 826 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain breaks: 2 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "E" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4526 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 27, 'TRANS': 557} Chain breaks: 3 Chain: "F" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4526 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 27, 'TRANS': 557} Chain breaks: 3 Chain: "G" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4552 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.92, per 1000 atoms: 0.20 Number of scatterers: 14506 At special positions: 0 Unit cell: (88.5, 92.04, 227.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 89 16.00 O 2856 8.00 N 2475 7.00 C 9085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 670.5 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 16 sheets defined 12.6% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'E' and resid 49 through 54 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 124 through 135 Processing helix chain 'E' and resid 161 through 173 Processing helix chain 'E' and resid 241 through 252 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 269 through 287 removed outlier: 3.803A pdb=" N GLN E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 Processing helix chain 'F' and resid 54 through 60 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 124 through 136 removed outlier: 3.523A pdb=" N SER F 136 " --> pdb=" O ILE F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 173 Processing helix chain 'F' and resid 241 through 252 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 269 through 286 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 54 through 59 removed outlier: 3.869A pdb=" N ILE G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 62 No H-bonds generated for 'chain 'G' and resid 60 through 62' Processing helix chain 'G' and resid 107 through 110 Processing helix chain 'G' and resid 125 through 135 Processing helix chain 'G' and resid 161 through 173 Processing helix chain 'G' and resid 241 through 252 Processing helix chain 'G' and resid 269 through 288 Processing helix chain 'G' and resid 389 through 391 No H-bonds generated for 'chain 'G' and resid 389 through 391' Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 14 removed outlier: 7.176A pdb=" N MET B 12 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 109 " --> pdb=" O MET B 12 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 14 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 39 current: chain 'E' and resid 417 through 420 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 417 through 420 current: chain 'E' and resid 472 through 476 removed outlier: 3.968A pdb=" N ILE E 487 " --> pdb=" O PHE E 495 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 503 through 507 current: chain 'F' and resid 417 through 420 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 417 through 420 current: chain 'F' and resid 472 through 476 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 503 through 516 current: chain 'G' and resid 417 through 420 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 417 through 420 current: chain 'G' and resid 472 through 476 Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 19 current: chain 'E' and resid 36 through 41 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 41 current: chain 'E' and resid 78 through 91 removed outlier: 3.683A pdb=" N SER E 86 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU E 103 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE E 88 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE E 101 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL E 90 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE E 99 " --> pdb=" O VAL E 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 99 through 105 current: chain 'E' and resid 289 through 295 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 289 through 295 current: chain 'E' and resid 340 through 347 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 340 through 347 current: chain 'F' and resid 36 through 41 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 36 through 41 current: chain 'F' and resid 99 through 103 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 99 through 103 current: chain 'F' and resid 289 through 295 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 289 through 295 current: chain 'F' and resid 321 through 334 removed outlier: 5.447A pdb=" N ILE F 327 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL F 347 " --> pdb=" O ILE F 327 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 340 through 348 current: chain 'G' and resid 18 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 19 current: chain 'G' and resid 36 through 41 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 36 through 41 current: chain 'G' and resid 78 through 92 removed outlier: 5.384A pdb=" N ILE G 85 " --> pdb=" O GLY G 105 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY G 105 " --> pdb=" O ILE G 85 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 99 through 105 current: chain 'G' and resid 289 through 295 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 289 through 295 current: chain 'G' and resid 321 through 334 removed outlier: 5.478A pdb=" N ILE G 327 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL G 347 " --> pdb=" O ILE G 327 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU G 329 " --> pdb=" O CYS G 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 116 through 123 removed outlier: 4.745A pdb=" N ALA E 116 " --> pdb=" O LYS E 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 141 through 144 removed outlier: 7.023A pdb=" N ASN E 141 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 186 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR E 143 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 228 through 233 Processing sheet with id=AA7, first strand: chain 'E' and resid 399 through 400 removed outlier: 6.618A pdb=" N LYS E 384 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU E 428 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER E 446 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET E 430 " --> pdb=" O THR E 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain 'F' and resid 116 through 123 removed outlier: 6.791A pdb=" N MET F 117 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR F 158 " --> pdb=" O MET F 117 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS F 119 " --> pdb=" O ALA F 156 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA F 156 " --> pdb=" O CYS F 119 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL F 121 " --> pdb=" O TYR F 154 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR F 154 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 142 through 144 removed outlier: 6.093A pdb=" N THR F 143 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 228 through 233 Processing sheet with id=AB3, first strand: chain 'F' and resid 399 through 400 removed outlier: 6.714A pdb=" N LYS F 384 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 428 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER F 446 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET F 430 " --> pdb=" O THR F 444 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 403 through 404 removed outlier: 6.728A pdb=" N MET G 430 " --> pdb=" O THR G 444 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER G 446 " --> pdb=" O LEU G 428 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU G 428 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS G 384 " --> pdb=" O VAL G 372 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 116 through 124 removed outlier: 6.717A pdb=" N MET G 117 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR G 158 " --> pdb=" O MET G 117 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS G 119 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA G 156 " --> pdb=" O CYS G 119 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL G 121 " --> pdb=" O TYR G 154 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR G 154 " --> pdb=" O VAL G 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 141 through 144 removed outlier: 6.719A pdb=" N ASN G 141 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE G 186 " --> pdb=" O ASN G 141 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR G 143 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 228 through 233 303 hydrogen bonds defined for protein. 807 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: 2.50 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4341 1.33 - 1.45: 2292 1.45 - 1.57: 8011 1.57 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 14797 Sorted by residual: bond pdb=" N VAL E 360 " pdb=" CA VAL E 360 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.82e+00 bond pdb=" N ASP E 56 " pdb=" CA ASP E 56 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.08e+00 bond pdb=" N MET E 354 " pdb=" CA MET E 354 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.25e-02 6.40e+03 8.48e+00 bond pdb=" N SER F 453 " pdb=" CA SER F 453 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.34e+00 bond pdb=" N VAL G 334 " pdb=" CA VAL G 334 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.92e+00 ... (remaining 14792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 19596 1.90 - 3.81: 388 3.81 - 5.71: 33 5.71 - 7.62: 1 7.62 - 9.52: 2 Bond angle restraints: 20020 Sorted by residual: angle pdb=" N GLN F 454 " pdb=" CA GLN F 454 " pdb=" C GLN F 454 " ideal model delta sigma weight residual 114.12 109.25 4.87 1.39e+00 5.18e-01 1.23e+01 angle pdb=" CA ASP F 459 " pdb=" C ASP F 459 " pdb=" O ASP F 459 " ideal model delta sigma weight residual 121.54 117.60 3.94 1.16e+00 7.43e-01 1.15e+01 angle pdb=" N PRO E 55 " pdb=" CA PRO E 55 " pdb=" C PRO E 55 " ideal model delta sigma weight residual 113.40 109.04 4.36 1.34e+00 5.57e-01 1.06e+01 angle pdb=" CA ALA F 456 " pdb=" C ALA F 456 " pdb=" O ALA F 456 " ideal model delta sigma weight residual 121.99 118.38 3.61 1.14e+00 7.69e-01 1.00e+01 angle pdb=" CA VAL E 353 " pdb=" C VAL E 353 " pdb=" O VAL E 353 " ideal model delta sigma weight residual 121.93 118.40 3.53 1.12e+00 7.97e-01 9.91e+00 ... (remaining 20015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7624 17.80 - 35.60: 837 35.60 - 53.41: 274 53.41 - 71.21: 80 71.21 - 89.01: 24 Dihedral angle restraints: 8839 sinusoidal: 3510 harmonic: 5329 Sorted by residual: dihedral pdb=" CA SER E 453 " pdb=" C SER E 453 " pdb=" N GLN E 454 " pdb=" CA GLN E 454 " ideal model delta harmonic sigma weight residual 180.00 150.10 29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASN E 452 " pdb=" C ASN E 452 " pdb=" N SER E 453 " pdb=" CA SER E 453 " ideal model delta harmonic sigma weight residual 180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA HIS F 34 " pdb=" C HIS F 34 " pdb=" N HIS F 35 " pdb=" CA HIS F 35 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1628 0.049 - 0.098: 383 0.098 - 0.147: 158 0.147 - 0.197: 19 0.197 - 0.246: 3 Chirality restraints: 2191 Sorted by residual: chirality pdb=" CA ASP E 56 " pdb=" N ASP E 56 " pdb=" C ASP E 56 " pdb=" CB ASP E 56 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE G 330 " pdb=" N ILE G 330 " pdb=" C ILE G 330 " pdb=" CB ILE G 330 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE F 330 " pdb=" N ILE F 330 " pdb=" C ILE F 330 " pdb=" CB ILE F 330 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2188 not shown) Planarity restraints: 2629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 347 " -0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO F 348 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 348 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 348 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 116 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 117 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 329 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C GLU G 329 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU G 329 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE G 330 " -0.009 2.00e-02 2.50e+03 ... (remaining 2626 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1224 2.74 - 3.28: 13493 3.28 - 3.82: 25767 3.82 - 4.36: 32135 4.36 - 4.90: 55000 Nonbonded interactions: 127619 Sorted by model distance: nonbonded pdb=" O ALA E 604 " pdb=" OG SER G 610 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASN F 216 " pdb=" OH TYR F 233 " model vdw 2.214 3.040 nonbonded pdb=" O ASN G 460 " pdb=" OG1 THR G 461 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASN E 216 " pdb=" OH TYR E 233 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASN E 124 " pdb=" OG1 THR E 127 " model vdw 2.234 3.040 ... (remaining 127614 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 'E' selection = chain 'F' selection = (chain 'G' and (resid 8 through 92 or resid 98 through 189 or resid 202 through \ 617)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.540 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.004 0.057 14797 Z= 0.234 Angle : 0.607 9.520 20020 Z= 0.356 Chirality : 0.050 0.246 2191 Planarity : 0.004 0.054 2629 Dihedral : 17.881 89.009 5447 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 23.63 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 1848 helix: 1.13 (0.36), residues: 212 sheet: -0.24 (0.24), residues: 452 loop : -1.46 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.012 0.001 TYR E 449 PHE 0.016 0.002 PHE F 37 TRP 0.012 0.002 TRP E 389 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00422 (14797) covalent geometry : angle 0.60702 (20020) hydrogen bonds : bond 0.13970 ( 303) hydrogen bonds : angle 6.51670 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.573 Fit side-chains REVERT: B 44 MET cc_start: 0.7215 (mmm) cc_final: 0.6932 (mmm) REVERT: B 84 MET cc_start: 0.7323 (ptm) cc_final: 0.6991 (ptp) REVERT: E 427 ASP cc_start: 0.8739 (m-30) cc_final: 0.8364 (m-30) REVERT: F 335 ASP cc_start: 0.6541 (p0) cc_final: 0.6307 (p0) REVERT: F 427 ASP cc_start: 0.8081 (m-30) cc_final: 0.7855 (m-30) REVERT: F 538 GLN cc_start: 0.8283 (tp40) cc_final: 0.8059 (tp40) REVERT: G 67 SER cc_start: 0.9015 (t) cc_final: 0.8814 (p) REVERT: G 220 TYR cc_start: 0.8820 (p90) cc_final: 0.8484 (p90) REVERT: G 249 LYS cc_start: 0.8312 (tttm) cc_final: 0.8082 (tptm) REVERT: G 309 ARG cc_start: 0.7570 (mtt90) cc_final: 0.7086 (mtt90) REVERT: G 345 CYS cc_start: 0.8211 (m) cc_final: 0.7949 (m) REVERT: G 427 ASP cc_start: 0.8631 (m-30) cc_final: 0.8291 (m-30) REVERT: G 537 MET cc_start: 0.8574 (ttm) cc_final: 0.8348 (ttm) REVERT: G 582 ASN cc_start: 0.8072 (m-40) cc_final: 0.7521 (m-40) REVERT: G 611 SER cc_start: 0.8583 (m) cc_final: 0.8310 (t) outliers start: 0 outliers final: 2 residues processed: 369 average time/residue: 0.6188 time to fit residues: 249.6957 Evaluate side-chains 220 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain G residue 321 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 113 GLN C 399 ASN E 29 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 HIS E 342 ASN F 42 ASN F 476 ASN F 526 GLN ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 ASN G 35 HIS G 82 HIS G 437 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100037 restraints weight = 20663.290| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.07 r_work: 0.3110 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 14797 Z= 0.262 Angle : 0.655 10.761 20020 Z= 0.344 Chirality : 0.050 0.172 2191 Planarity : 0.005 0.048 2629 Dihedral : 5.857 122.919 2015 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.79 % Allowed : 23.19 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.18), residues: 1848 helix: 0.77 (0.35), residues: 227 sheet: -0.36 (0.24), residues: 444 loop : -1.43 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 245 TYR 0.017 0.002 TYR G 449 PHE 0.018 0.002 PHE E 419 TRP 0.017 0.002 TRP G 356 HIS 0.008 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00624 (14797) covalent geometry : angle 0.65540 (20020) hydrogen bonds : bond 0.04686 ( 303) hydrogen bonds : angle 5.51263 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 228 time to evaluate : 0.601 Fit side-chains REVERT: B 44 MET cc_start: 0.7502 (mmm) cc_final: 0.7039 (mmm) REVERT: C 401 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6447 (p) REVERT: E 47 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6752 (mtmm) REVERT: E 139 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8012 (ptmt) REVERT: E 182 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7895 (pp20) REVERT: E 244 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8264 (p) REVERT: E 565 LYS cc_start: 0.7542 (tttm) cc_final: 0.6743 (tppt) REVERT: E 579 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8921 (t) REVERT: E 586 ASP cc_start: 0.8187 (t0) cc_final: 0.7785 (m-30) REVERT: E 603 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8023 (t0) REVERT: F 38 LYS cc_start: 0.8585 (tttt) cc_final: 0.8139 (ttmp) REVERT: F 292 LYS cc_start: 0.8642 (mttt) cc_final: 0.7813 (mtmt) REVERT: F 309 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7115 (mtm180) REVERT: F 347 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8816 (p) REVERT: F 538 GLN cc_start: 0.8536 (tp40) cc_final: 0.8277 (tp40) REVERT: F 552 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: F 612 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: G 12 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7387 (pt0) REVERT: G 67 SER cc_start: 0.9064 (t) cc_final: 0.8783 (p) REVERT: G 91 GLU cc_start: 0.8118 (pt0) cc_final: 0.7855 (pt0) REVERT: G 221 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8549 (tp30) REVERT: G 228 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7369 (mttp) REVERT: G 249 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7943 (tptm) REVERT: G 292 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8124 (ttpp) REVERT: G 309 ARG cc_start: 0.7730 (mtt90) cc_final: 0.7218 (mtt180) REVERT: G 427 ASP cc_start: 0.8916 (m-30) cc_final: 0.8495 (m-30) REVERT: G 482 ASP cc_start: 0.8392 (m-30) cc_final: 0.8011 (m-30) REVERT: G 505 GLU cc_start: 0.8478 (tt0) cc_final: 0.8199 (tt0) REVERT: G 561 GLU cc_start: 0.7879 (tt0) cc_final: 0.7603 (tt0) REVERT: G 588 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.6831 (tm-30) outliers start: 108 outliers final: 35 residues processed: 311 average time/residue: 0.6341 time to fit residues: 215.8622 Evaluate side-chains 239 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 368 MET Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 612 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 249 LYS Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 593 THR Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 142 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101829 restraints weight = 20754.848| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.07 r_work: 0.3135 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14797 Z= 0.140 Angle : 0.542 10.519 20020 Z= 0.281 Chirality : 0.046 0.151 2191 Planarity : 0.004 0.041 2629 Dihedral : 4.526 30.307 2010 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.78 % Allowed : 24.76 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 1848 helix: 0.97 (0.35), residues: 233 sheet: -0.34 (0.24), residues: 431 loop : -1.38 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 245 TYR 0.013 0.001 TYR F 449 PHE 0.017 0.001 PHE B 31 TRP 0.013 0.001 TRP F 389 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00321 (14797) covalent geometry : angle 0.54189 (20020) hydrogen bonds : bond 0.03808 ( 303) hydrogen bonds : angle 5.26283 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 215 time to evaluate : 0.424 Fit side-chains REVERT: B 14 MET cc_start: 0.6139 (ptm) cc_final: 0.5787 (ptt) REVERT: B 44 MET cc_start: 0.7551 (mmm) cc_final: 0.7021 (mmm) REVERT: E 47 LYS cc_start: 0.7034 (mmtt) cc_final: 0.6622 (mtmm) REVERT: E 244 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (p) REVERT: E 305 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8956 (mp) REVERT: E 324 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7053 (mmm-85) REVERT: E 505 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: E 565 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6550 (mptt) REVERT: E 586 ASP cc_start: 0.8141 (t0) cc_final: 0.7886 (m-30) REVERT: E 590 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7869 (mtm) REVERT: E 603 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7931 (t0) REVERT: F 38 LYS cc_start: 0.8624 (tttt) cc_final: 0.8194 (ttmp) REVERT: F 51 TRP cc_start: 0.8781 (m100) cc_final: 0.8577 (m100) REVERT: F 91 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: F 292 LYS cc_start: 0.8607 (mttt) cc_final: 0.7810 (mtmt) REVERT: F 309 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7296 (mtm110) REVERT: F 427 ASP cc_start: 0.8059 (m-30) cc_final: 0.7737 (m-30) REVERT: F 538 GLN cc_start: 0.8552 (tp40) cc_final: 0.8260 (tp40) REVERT: F 552 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: F 555 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8532 (mm) REVERT: F 612 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: G 58 ILE cc_start: 0.8257 (mm) cc_final: 0.8035 (mt) REVERT: G 67 SER cc_start: 0.9103 (t) cc_final: 0.8901 (p) REVERT: G 91 GLU cc_start: 0.8164 (pt0) cc_final: 0.7789 (pt0) REVERT: G 112 ASP cc_start: 0.8621 (t0) cc_final: 0.8357 (t0) REVERT: G 228 LYS cc_start: 0.7979 (mmpt) cc_final: 0.7259 (mttp) REVERT: G 249 LYS cc_start: 0.8420 (tttm) cc_final: 0.7945 (tptm) REVERT: G 274 GLU cc_start: 0.7511 (pt0) cc_final: 0.7263 (pt0) REVERT: G 292 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8063 (ttpp) REVERT: G 309 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7390 (mtt90) REVERT: G 368 MET cc_start: 0.9096 (mtm) cc_final: 0.8762 (mtm) REVERT: G 427 ASP cc_start: 0.8856 (m-30) cc_final: 0.8356 (m-30) REVERT: G 482 ASP cc_start: 0.8371 (m-30) cc_final: 0.8042 (t0) REVERT: G 505 GLU cc_start: 0.8457 (tt0) cc_final: 0.8152 (tt0) REVERT: G 561 GLU cc_start: 0.7838 (tt0) cc_final: 0.7556 (tt0) outliers start: 76 outliers final: 31 residues processed: 268 average time/residue: 0.6227 time to fit residues: 182.4773 Evaluate side-chains 235 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 555 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 612 GLU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 148 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN G 569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105308 restraints weight = 20126.810| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.98 r_work: 0.3198 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14797 Z= 0.202 Angle : 0.579 10.022 20020 Z= 0.300 Chirality : 0.047 0.162 2191 Planarity : 0.004 0.048 2629 Dihedral : 4.635 30.420 2010 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.97 % Allowed : 24.95 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 1848 helix: 1.06 (0.36), residues: 227 sheet: -0.36 (0.24), residues: 444 loop : -1.36 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 245 TYR 0.014 0.001 TYR E 449 PHE 0.016 0.002 PHE B 31 TRP 0.012 0.002 TRP G 356 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00472 (14797) covalent geometry : angle 0.57890 (20020) hydrogen bonds : bond 0.04057 ( 303) hydrogen bonds : angle 5.31700 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 0.624 Fit side-chains REVERT: B 5 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 44 MET cc_start: 0.7585 (mmm) cc_final: 0.7073 (mmm) REVERT: B 111 THR cc_start: 0.7774 (p) cc_final: 0.7209 (t) REVERT: C 403 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7581 (mtmm) REVERT: E 47 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6627 (mtmm) REVERT: E 305 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9004 (mp) REVERT: E 324 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7193 (mmm-85) REVERT: E 565 LYS cc_start: 0.7673 (tttm) cc_final: 0.6720 (mptt) REVERT: E 579 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9022 (t) REVERT: E 586 ASP cc_start: 0.8270 (t0) cc_final: 0.8047 (m-30) REVERT: E 590 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7864 (mtm) REVERT: E 603 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8031 (t0) REVERT: F 38 LYS cc_start: 0.8784 (tttt) cc_final: 0.8441 (ttmp) REVERT: F 51 TRP cc_start: 0.8724 (m100) cc_final: 0.8490 (m100) REVERT: F 91 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: F 271 MET cc_start: 0.8030 (tpt) cc_final: 0.7798 (tpt) REVERT: F 292 LYS cc_start: 0.8721 (mttt) cc_final: 0.8078 (mtmt) REVERT: F 309 ARG cc_start: 0.7739 (mtm110) cc_final: 0.7406 (mtm110) REVERT: F 538 GLN cc_start: 0.8590 (tp40) cc_final: 0.8379 (tp40) REVERT: F 552 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: F 555 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8637 (mm) REVERT: F 612 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: G 67 SER cc_start: 0.9108 (t) cc_final: 0.8897 (p) REVERT: G 91 GLU cc_start: 0.8060 (pt0) cc_final: 0.7774 (pt0) REVERT: G 228 LYS cc_start: 0.8185 (mmpt) cc_final: 0.7624 (mttp) REVERT: G 249 LYS cc_start: 0.8483 (tttm) cc_final: 0.8013 (tptm) REVERT: G 292 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8278 (ttpp) REVERT: G 309 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7342 (mtt90) REVERT: G 368 MET cc_start: 0.9183 (mtm) cc_final: 0.8852 (mtm) REVERT: G 427 ASP cc_start: 0.8792 (m-30) cc_final: 0.8224 (m-30) REVERT: G 482 ASP cc_start: 0.8433 (m-30) cc_final: 0.8132 (t0) REVERT: G 505 GLU cc_start: 0.8446 (tt0) cc_final: 0.8170 (tt0) REVERT: G 561 GLU cc_start: 0.7774 (tt0) cc_final: 0.7526 (tt0) REVERT: G 588 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: G 589 ASP cc_start: 0.8302 (m-30) cc_final: 0.8033 (m-30) outliers start: 79 outliers final: 50 residues processed: 264 average time/residue: 0.5927 time to fit residues: 172.3001 Evaluate side-chains 249 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 555 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 612 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 534 GLU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 593 THR Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104779 restraints weight = 20208.742| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.97 r_work: 0.3189 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14797 Z= 0.214 Angle : 0.582 10.474 20020 Z= 0.302 Chirality : 0.048 0.175 2191 Planarity : 0.004 0.055 2629 Dihedral : 4.672 31.145 2010 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.10 % Allowed : 24.76 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 1848 helix: 1.18 (0.36), residues: 221 sheet: -0.38 (0.24), residues: 444 loop : -1.42 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 245 TYR 0.015 0.002 TYR F 173 PHE 0.019 0.002 PHE B 31 TRP 0.012 0.002 TRP G 356 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00503 (14797) covalent geometry : angle 0.58214 (20020) hydrogen bonds : bond 0.04014 ( 303) hydrogen bonds : angle 5.30329 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 197 time to evaluate : 0.585 Fit side-chains REVERT: B 44 MET cc_start: 0.7665 (mmm) cc_final: 0.7091 (mmm) REVERT: B 85 MET cc_start: 0.7173 (mpp) cc_final: 0.6968 (mmt) REVERT: B 111 THR cc_start: 0.7882 (p) cc_final: 0.7406 (t) REVERT: E 47 LYS cc_start: 0.7094 (mmtt) cc_final: 0.6611 (mtmm) REVERT: E 260 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8607 (mtmm) REVERT: E 305 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8946 (mp) REVERT: E 324 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7166 (mmm-85) REVERT: E 435 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: E 565 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6768 (mptt) REVERT: E 579 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9020 (t) REVERT: E 590 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: F 38 LYS cc_start: 0.8883 (tttt) cc_final: 0.8438 (ttmp) REVERT: F 91 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: F 271 MET cc_start: 0.8069 (tpt) cc_final: 0.7819 (tpt) REVERT: F 292 LYS cc_start: 0.8764 (mttt) cc_final: 0.8242 (mttp) REVERT: F 309 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7556 (mtm110) REVERT: F 552 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: F 555 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8642 (mm) REVERT: G 67 SER cc_start: 0.9128 (t) cc_final: 0.8916 (p) REVERT: G 91 GLU cc_start: 0.8121 (pt0) cc_final: 0.7814 (pt0) REVERT: G 112 ASP cc_start: 0.8605 (t0) cc_final: 0.8337 (t0) REVERT: G 221 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8395 (tp30) REVERT: G 228 LYS cc_start: 0.8200 (mmpt) cc_final: 0.7659 (mttp) REVERT: G 249 LYS cc_start: 0.8459 (tttm) cc_final: 0.7978 (tptm) REVERT: G 292 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8296 (ttpp) REVERT: G 309 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7420 (mtt90) REVERT: G 368 MET cc_start: 0.9224 (mtm) cc_final: 0.8905 (mtm) REVERT: G 482 ASP cc_start: 0.8407 (m-30) cc_final: 0.8071 (t0) REVERT: G 561 GLU cc_start: 0.7727 (tt0) cc_final: 0.7483 (tt0) REVERT: G 588 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: G 589 ASP cc_start: 0.8357 (m-30) cc_final: 0.8096 (m-30) outliers start: 97 outliers final: 54 residues processed: 269 average time/residue: 0.5947 time to fit residues: 175.5388 Evaluate side-chains 256 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain E residue 566 ASP Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 555 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 489 ASP Chi-restraints excluded: chain G residue 534 GLU Chi-restraints excluded: chain G residue 537 MET Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 593 THR Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 85 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.0000 chunk 137 optimal weight: 2.9990 chunk 176 optimal weight: 0.0570 chunk 102 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 HIS F 42 ASN F 538 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108693 restraints weight = 20072.458| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.97 r_work: 0.3249 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14797 Z= 0.100 Angle : 0.516 10.510 20020 Z= 0.264 Chirality : 0.046 0.158 2191 Planarity : 0.004 0.057 2629 Dihedral : 4.276 28.534 2010 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.27 % Allowed : 26.71 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.19), residues: 1848 helix: 1.28 (0.36), residues: 227 sheet: -0.33 (0.24), residues: 443 loop : -1.33 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 245 TYR 0.012 0.001 TYR G 231 PHE 0.014 0.001 PHE F 37 TRP 0.013 0.001 TRP F 389 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00226 (14797) covalent geometry : angle 0.51557 (20020) hydrogen bonds : bond 0.03208 ( 303) hydrogen bonds : angle 5.00537 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.558 Fit side-chains REVERT: B 10 LYS cc_start: 0.6620 (mmtt) cc_final: 0.6380 (mmtt) REVERT: B 44 MET cc_start: 0.7646 (mmm) cc_final: 0.7249 (mmm) REVERT: B 85 MET cc_start: 0.6906 (mpp) cc_final: 0.6669 (mmt) REVERT: B 93 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8596 (tptp) REVERT: B 111 THR cc_start: 0.7736 (p) cc_final: 0.7440 (p) REVERT: B 122 MET cc_start: 0.5477 (mmt) cc_final: 0.5096 (mmm) REVERT: C 405 MET cc_start: 0.6646 (ptp) cc_final: 0.6075 (ptt) REVERT: E 135 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8395 (mttt) REVERT: E 274 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: E 305 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8929 (mp) REVERT: E 324 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7173 (mmm-85) REVERT: E 565 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6736 (mptt) REVERT: F 10 SER cc_start: 0.8247 (t) cc_final: 0.7410 (p) REVERT: F 38 LYS cc_start: 0.8842 (tttt) cc_final: 0.8399 (ttmp) REVERT: F 74 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8320 (mm-30) REVERT: F 91 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: F 271 MET cc_start: 0.7996 (tpt) cc_final: 0.7770 (tpt) REVERT: F 292 LYS cc_start: 0.8639 (mttt) cc_final: 0.8154 (mttp) REVERT: F 309 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7515 (mtm110) REVERT: F 525 GLU cc_start: 0.8264 (tt0) cc_final: 0.8024 (mt-10) REVERT: F 552 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: G 42 ASN cc_start: 0.7926 (t0) cc_final: 0.7704 (m-40) REVERT: G 67 SER cc_start: 0.9190 (t) cc_final: 0.8968 (p) REVERT: G 91 GLU cc_start: 0.8045 (pt0) cc_final: 0.7752 (pt0) REVERT: G 221 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: G 228 LYS cc_start: 0.8150 (mmpt) cc_final: 0.7546 (mttp) REVERT: G 249 LYS cc_start: 0.8654 (tttm) cc_final: 0.8174 (tptm) REVERT: G 292 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8213 (ttpp) REVERT: G 309 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7281 (mtt90) REVERT: G 368 MET cc_start: 0.9144 (mtm) cc_final: 0.8860 (mtm) REVERT: G 427 ASP cc_start: 0.8660 (m-30) cc_final: 0.8069 (m-30) REVERT: G 482 ASP cc_start: 0.8322 (m-30) cc_final: 0.8022 (t0) REVERT: G 534 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: G 561 GLU cc_start: 0.7738 (tt0) cc_final: 0.7522 (tt0) REVERT: G 563 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8905 (mt) REVERT: G 588 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: G 589 ASP cc_start: 0.8203 (m-30) cc_final: 0.7992 (m-30) outliers start: 68 outliers final: 28 residues processed: 260 average time/residue: 0.5946 time to fit residues: 170.0995 Evaluate side-chains 235 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 534 GLU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 563 ILE Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN F 42 ASN F 538 GLN ** G 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104457 restraints weight = 20120.171| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.97 r_work: 0.3190 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14797 Z= 0.220 Angle : 0.587 10.212 20020 Z= 0.305 Chirality : 0.048 0.166 2191 Planarity : 0.004 0.056 2629 Dihedral : 4.580 29.815 2010 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.71 % Allowed : 27.09 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1848 helix: 1.21 (0.36), residues: 227 sheet: -0.38 (0.24), residues: 456 loop : -1.38 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 44 TYR 0.017 0.002 TYR F 173 PHE 0.016 0.002 PHE E 543 TRP 0.014 0.002 TRP G 356 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00517 (14797) covalent geometry : angle 0.58658 (20020) hydrogen bonds : bond 0.03942 ( 303) hydrogen bonds : angle 5.20444 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.551 Fit side-chains REVERT: B 31 PHE cc_start: 0.7456 (t80) cc_final: 0.7255 (t80) REVERT: B 44 MET cc_start: 0.7664 (mmm) cc_final: 0.7275 (mmm) REVERT: B 93 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (tptp) REVERT: B 111 THR cc_start: 0.8005 (p) cc_final: 0.7532 (t) REVERT: C 405 MET cc_start: 0.6925 (ptp) cc_final: 0.6199 (ptt) REVERT: E 74 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: E 135 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8369 (mttt) REVERT: E 301 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7865 (ptp-170) REVERT: E 305 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9040 (mp) REVERT: E 324 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7191 (mmm-85) REVERT: E 435 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: E 505 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: E 565 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.6951 (tppt) REVERT: E 603 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7872 (t0) REVERT: F 10 SER cc_start: 0.8237 (t) cc_final: 0.7411 (p) REVERT: F 38 LYS cc_start: 0.8779 (tttt) cc_final: 0.8406 (ttmp) REVERT: F 91 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: F 292 LYS cc_start: 0.8678 (mttt) cc_final: 0.8184 (mttp) REVERT: F 309 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7688 (mtm110) REVERT: F 525 GLU cc_start: 0.8406 (tt0) cc_final: 0.8127 (mt-10) REVERT: F 552 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: G 42 ASN cc_start: 0.8025 (t0) cc_final: 0.7801 (m-40) REVERT: G 67 SER cc_start: 0.9141 (t) cc_final: 0.8937 (p) REVERT: G 91 GLU cc_start: 0.8104 (pt0) cc_final: 0.7815 (pt0) REVERT: G 190 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7614 (tm-30) REVERT: G 221 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: G 228 LYS cc_start: 0.8192 (mmpt) cc_final: 0.7637 (mttp) REVERT: G 249 LYS cc_start: 0.8459 (tttm) cc_final: 0.7972 (tptm) REVERT: G 292 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8338 (ttpp) REVERT: G 309 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7415 (mtt90) REVERT: G 368 MET cc_start: 0.9254 (mtm) cc_final: 0.9011 (mtm) REVERT: G 482 ASP cc_start: 0.8348 (m-30) cc_final: 0.8033 (t0) REVERT: G 561 GLU cc_start: 0.7742 (tt0) cc_final: 0.7533 (tt0) REVERT: G 563 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8960 (mt) REVERT: G 588 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: G 589 ASP cc_start: 0.8427 (m-30) cc_final: 0.8171 (m-30) outliers start: 75 outliers final: 46 residues processed: 252 average time/residue: 0.5754 time to fit residues: 159.9558 Evaluate side-chains 244 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 563 ILE Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 593 THR Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 185 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 538 GLN ** G 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106238 restraints weight = 20142.240| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.95 r_work: 0.3219 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14797 Z= 0.140 Angle : 0.545 10.400 20020 Z= 0.281 Chirality : 0.046 0.153 2191 Planarity : 0.004 0.056 2629 Dihedral : 4.416 29.121 2010 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.09 % Allowed : 27.47 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.19), residues: 1848 helix: 1.71 (0.37), residues: 209 sheet: -0.41 (0.24), residues: 451 loop : -1.36 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 44 TYR 0.014 0.001 TYR F 220 PHE 0.015 0.001 PHE F 37 TRP 0.013 0.001 TRP F 389 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00323 (14797) covalent geometry : angle 0.54460 (20020) hydrogen bonds : bond 0.03460 ( 303) hydrogen bonds : angle 5.09378 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.657 Fit side-chains REVERT: B 5 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8143 (mt-10) REVERT: B 44 MET cc_start: 0.7788 (mmm) cc_final: 0.7356 (mmm) REVERT: B 93 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8529 (tptp) REVERT: B 111 THR cc_start: 0.7946 (p) cc_final: 0.7545 (t) REVERT: C 403 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7329 (mtmm) REVERT: C 405 MET cc_start: 0.6813 (ptp) cc_final: 0.6293 (ptt) REVERT: E 23 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8752 (m) REVERT: E 135 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8362 (mttt) REVERT: E 274 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: E 301 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7802 (ptp-170) REVERT: E 309 ARG cc_start: 0.6023 (ptt-90) cc_final: 0.5738 (ptt90) REVERT: E 324 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7190 (mmm-85) REVERT: E 561 GLU cc_start: 0.8374 (pt0) cc_final: 0.7953 (pp20) REVERT: E 565 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6957 (tppt) REVERT: F 10 SER cc_start: 0.8241 (t) cc_final: 0.7425 (p) REVERT: F 38 LYS cc_start: 0.8782 (tttt) cc_final: 0.8404 (ttmp) REVERT: F 91 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: F 292 LYS cc_start: 0.8650 (mttt) cc_final: 0.8167 (mttp) REVERT: F 525 GLU cc_start: 0.8369 (tt0) cc_final: 0.8081 (mt-10) REVERT: F 552 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: G 42 ASN cc_start: 0.8036 (t0) cc_final: 0.7810 (m-40) REVERT: G 67 SER cc_start: 0.9190 (t) cc_final: 0.8938 (p) REVERT: G 91 GLU cc_start: 0.8094 (pt0) cc_final: 0.7804 (pt0) REVERT: G 190 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7585 (tm-30) REVERT: G 221 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: G 228 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7571 (mttp) REVERT: G 249 LYS cc_start: 0.8675 (tttm) cc_final: 0.8196 (tptm) REVERT: G 292 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8320 (ttpp) REVERT: G 358 ASP cc_start: 0.7727 (t70) cc_final: 0.7440 (t0) REVERT: G 368 MET cc_start: 0.9215 (mtm) cc_final: 0.8985 (mtm) REVERT: G 427 ASP cc_start: 0.8757 (m-30) cc_final: 0.8221 (m-30) REVERT: G 482 ASP cc_start: 0.8355 (m-30) cc_final: 0.8047 (t0) REVERT: G 563 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8922 (mt) REVERT: G 588 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: G 589 ASP cc_start: 0.8363 (m-30) cc_final: 0.8120 (m-30) outliers start: 65 outliers final: 40 residues processed: 246 average time/residue: 0.6252 time to fit residues: 168.9293 Evaluate side-chains 240 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 614 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 292 LYS Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 563 ILE Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 593 THR Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 42 optimal weight: 3.9990 chunk 110 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 538 GLN ** G 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107687 restraints weight = 20056.854| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.95 r_work: 0.3238 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14797 Z= 0.118 Angle : 0.533 10.307 20020 Z= 0.274 Chirality : 0.046 0.149 2191 Planarity : 0.004 0.057 2629 Dihedral : 4.263 27.666 2010 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.77 % Allowed : 28.41 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1848 helix: 1.66 (0.37), residues: 215 sheet: -0.36 (0.24), residues: 453 loop : -1.36 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 44 TYR 0.015 0.001 TYR F 220 PHE 0.014 0.001 PHE F 37 TRP 0.011 0.001 TRP F 389 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00271 (14797) covalent geometry : angle 0.53272 (20020) hydrogen bonds : bond 0.03244 ( 303) hydrogen bonds : angle 4.95291 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.7768 (mmm) cc_final: 0.7395 (mmm) REVERT: B 93 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8545 (tptp) REVERT: B 111 THR cc_start: 0.7951 (p) cc_final: 0.7554 (t) REVERT: C 405 MET cc_start: 0.6840 (ptp) cc_final: 0.6284 (ptt) REVERT: E 23 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8726 (m) REVERT: E 74 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: E 118 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8515 (t0) REVERT: E 135 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8360 (mttt) REVERT: E 260 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8644 (mtmm) REVERT: E 274 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: E 301 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7817 (ptp-170) REVERT: E 309 ARG cc_start: 0.5995 (ptt-90) cc_final: 0.5704 (ptt90) REVERT: E 561 GLU cc_start: 0.8416 (pt0) cc_final: 0.8001 (pp20) REVERT: F 10 SER cc_start: 0.8127 (t) cc_final: 0.7430 (p) REVERT: F 38 LYS cc_start: 0.8793 (tttt) cc_final: 0.8401 (ttmp) REVERT: F 42 ASN cc_start: 0.7826 (t0) cc_final: 0.7614 (t0) REVERT: F 91 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: F 292 LYS cc_start: 0.8637 (mttt) cc_final: 0.8160 (mttp) REVERT: F 331 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8181 (m) REVERT: F 525 GLU cc_start: 0.8380 (tt0) cc_final: 0.8075 (mt-10) REVERT: F 552 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: G 42 ASN cc_start: 0.8001 (t0) cc_final: 0.7784 (m-40) REVERT: G 67 SER cc_start: 0.9199 (t) cc_final: 0.8976 (p) REVERT: G 91 GLU cc_start: 0.8090 (pt0) cc_final: 0.7799 (pt0) REVERT: G 190 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7649 (tm-30) REVERT: G 221 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: G 228 LYS cc_start: 0.8136 (mmpt) cc_final: 0.7543 (mttp) REVERT: G 249 LYS cc_start: 0.8659 (tttm) cc_final: 0.8183 (tptm) REVERT: G 292 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8272 (ttpp) REVERT: G 358 ASP cc_start: 0.7801 (t70) cc_final: 0.7537 (t0) REVERT: G 368 MET cc_start: 0.9187 (mtm) cc_final: 0.8942 (mtm) REVERT: G 427 ASP cc_start: 0.8649 (m-30) cc_final: 0.8076 (m-30) REVERT: G 482 ASP cc_start: 0.8346 (m-30) cc_final: 0.8042 (t0) REVERT: G 563 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8934 (mt) REVERT: G 588 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: G 589 ASP cc_start: 0.8293 (m-30) cc_final: 0.8046 (m-30) outliers start: 60 outliers final: 38 residues processed: 244 average time/residue: 0.6139 time to fit residues: 165.2903 Evaluate side-chains 240 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 420 VAL Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 563 ILE Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 593 THR Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN F 526 GLN F 528 ASN F 538 GLN ** G 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108159 restraints weight = 20097.788| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.95 r_work: 0.3245 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14797 Z= 0.116 Angle : 0.543 10.330 20020 Z= 0.278 Chirality : 0.046 0.149 2191 Planarity : 0.004 0.057 2629 Dihedral : 4.233 26.985 2010 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.71 % Allowed : 28.85 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1848 helix: 1.71 (0.37), residues: 215 sheet: -0.37 (0.24), residues: 451 loop : -1.34 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 44 TYR 0.018 0.001 TYR F 220 PHE 0.014 0.001 PHE F 37 TRP 0.012 0.001 TRP F 389 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00267 (14797) covalent geometry : angle 0.54314 (20020) hydrogen bonds : bond 0.03224 ( 303) hydrogen bonds : angle 4.92209 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 12 MET cc_start: 0.6214 (OUTLIER) cc_final: 0.5981 (ptp) REVERT: B 44 MET cc_start: 0.7755 (mmm) cc_final: 0.7380 (mmm) REVERT: B 85 MET cc_start: 0.6773 (mmt) cc_final: 0.6127 (mmm) REVERT: B 93 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8548 (tptp) REVERT: B 111 THR cc_start: 0.7895 (p) cc_final: 0.7672 (p) REVERT: C 405 MET cc_start: 0.6845 (ptp) cc_final: 0.6313 (ptt) REVERT: E 23 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8718 (m) REVERT: E 74 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: E 135 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8369 (mttt) REVERT: E 185 GLN cc_start: 0.8675 (tp40) cc_final: 0.8449 (tm-30) REVERT: E 260 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (mtmm) REVERT: E 274 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: E 301 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7807 (ptp-170) REVERT: E 309 ARG cc_start: 0.5961 (ptt-90) cc_final: 0.5687 (ptt90) REVERT: E 561 GLU cc_start: 0.8419 (pt0) cc_final: 0.8010 (pp20) REVERT: F 10 SER cc_start: 0.8092 (t) cc_final: 0.7391 (p) REVERT: F 38 LYS cc_start: 0.8797 (tttt) cc_final: 0.8399 (ttmp) REVERT: F 292 LYS cc_start: 0.8629 (mttt) cc_final: 0.8148 (mttp) REVERT: F 331 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8167 (m) REVERT: F 339 ARG cc_start: 0.6395 (tpm170) cc_final: 0.5909 (tpp80) REVERT: F 525 GLU cc_start: 0.8421 (tt0) cc_final: 0.8126 (mt-10) REVERT: F 552 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: G 47 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7689 (mptt) REVERT: G 67 SER cc_start: 0.9196 (t) cc_final: 0.8968 (p) REVERT: G 91 GLU cc_start: 0.8083 (pt0) cc_final: 0.7718 (pt0) REVERT: G 190 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7658 (tm-30) REVERT: G 221 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8344 (tp30) REVERT: G 228 LYS cc_start: 0.8130 (mmpt) cc_final: 0.7524 (mttp) REVERT: G 249 LYS cc_start: 0.8658 (tttm) cc_final: 0.8183 (tptm) REVERT: G 292 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8258 (ttpp) REVERT: G 358 ASP cc_start: 0.7794 (t70) cc_final: 0.7543 (t0) REVERT: G 368 MET cc_start: 0.9179 (mtm) cc_final: 0.8933 (mtm) REVERT: G 427 ASP cc_start: 0.8691 (m-30) cc_final: 0.8114 (m-30) REVERT: G 482 ASP cc_start: 0.8394 (m-30) cc_final: 0.8125 (t0) REVERT: G 563 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8924 (mt) REVERT: G 588 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: G 589 ASP cc_start: 0.8173 (m-30) cc_final: 0.7951 (m-30) outliers start: 59 outliers final: 35 residues processed: 241 average time/residue: 0.6319 time to fit residues: 167.3168 Evaluate side-chains 236 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 278 ASP Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 552 GLU Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 375 GLU Chi-restraints excluded: chain G residue 474 GLU Chi-restraints excluded: chain G residue 563 ILE Chi-restraints excluded: chain G residue 588 GLN Chi-restraints excluded: chain G residue 612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 GLN ** G 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104597 restraints weight = 20162.414| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.94 r_work: 0.3193 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14797 Z= 0.215 Angle : 0.601 10.223 20020 Z= 0.312 Chirality : 0.047 0.162 2191 Planarity : 0.004 0.056 2629 Dihedral : 4.529 28.764 2010 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.83 % Allowed : 28.79 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1848 helix: 1.59 (0.37), residues: 215 sheet: -0.40 (0.24), residues: 456 loop : -1.41 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 44 TYR 0.019 0.002 TYR F 220 PHE 0.016 0.002 PHE E 495 TRP 0.013 0.002 TRP F 389 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00508 (14797) covalent geometry : angle 0.60094 (20020) hydrogen bonds : bond 0.03857 ( 303) hydrogen bonds : angle 5.11728 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.70 seconds wall clock time: 92 minutes 3.98 seconds (5523.98 seconds total)