Starting phenix.real_space_refine on Sun Aug 24 07:04:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcu_15968/08_2025/8bcu_15968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcu_15968/08_2025/8bcu_15968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bcu_15968/08_2025/8bcu_15968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcu_15968/08_2025/8bcu_15968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bcu_15968/08_2025/8bcu_15968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcu_15968/08_2025/8bcu_15968.map" } resolution = 4.05 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= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 11475 2.51 5 N 3051 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18279 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 150} Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "H" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 150} Chain: "B" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "G" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "E" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 150} Chain: "F" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Time building chain proxies: 3.90, per 1000 atoms: 0.21 Number of scatterers: 18279 At special positions: 0 Unit cell: (154.014, 163.471, 104.027, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3687 8.00 N 3051 7.00 C 11475 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: 1.24 Conformation dependent library (CDL) restraints added in 562.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 30 sheets defined 16.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 85 through 103 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'H' and resid 5 through 7 No H-bonds generated for 'chain 'H' and resid 5 through 7' Processing helix chain 'H' and resid 91 through 100 Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'H' and resid 192 through 201 removed outlier: 4.083A pdb=" N GLY H 201 " --> pdb=" O MET H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 287 removed outlier: 3.523A pdb=" N LEU H 287 " --> pdb=" O LEU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 85 through 103 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'G' and resid 192 through 201 removed outlier: 4.325A pdb=" N GLY G 201 " --> pdb=" O MET G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 287 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 85 through 103 Processing helix chain 'F' and resid 3 through 18 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 85 through 103 Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 91 through 100 Processing helix chain 'I' and resid 185 through 190 Processing helix chain 'I' and resid 192 through 201 removed outlier: 4.165A pdb=" N GLY I 201 " --> pdb=" O MET I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 287 Processing helix chain 'I' and resid 358 through 369 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.007A pdb=" N SER C 36 " --> pdb=" O VAL C 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 53 current: chain 'C' and resid 70 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 70 through 73 current: chain 'C' and resid 141 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 152 current: chain 'D' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 53 current: chain 'D' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 72 current: chain 'D' and resid 141 through 148 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 141 through 148 current: chain 'A' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 53 current: chain 'A' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 73 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'B' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 53 current: chain 'B' and resid 68 through 81 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 81 current: chain 'B' and resid 141 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 152 current: chain 'E' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 53 current: chain 'E' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 73 current: chain 'E' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 152 current: chain 'F' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 53 current: chain 'F' and resid 68 through 81 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 81 current: chain 'F' and resid 141 through 152 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AA3, first strand: chain 'D' and resid 109 through 111 Processing sheet with id=AA4, first strand: chain 'H' and resid 25 through 28 removed outlier: 4.314A pdb=" N ILE H 11 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 14 " --> pdb=" O HIS H 135 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP H 144 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 71 current: chain 'H' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 119 through 122 current: chain 'H' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 166 through 173 current: chain 'H' and resid 220 through 224 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 220 through 224 current: chain 'H' and resid 261 through 268 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 261 through 268 current: chain 'H' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 307 through 319 current: chain 'H' and resid 331 through 338 Processing sheet with id=AA6, first strand: chain 'H' and resid 43 through 46 Processing sheet with id=AA7, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.735A pdb=" N LYS H 86 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 378 through 382 removed outlier: 3.517A pdb=" N THR H 380 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 389 through 391 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 389 through 391 current: chain 'H' and resid 440 through 446 removed outlier: 3.936A pdb=" N ALA H 444 " --> pdb=" O GLY H 454 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY H 454 " --> pdb=" O ALA H 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 395 through 396 Processing sheet with id=AB2, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB4, first strand: chain 'G' and resid 25 through 28 removed outlier: 4.368A pdb=" N ILE G 11 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE G 136 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP G 144 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 75 current: chain 'G' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 119 through 122 current: chain 'G' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 173 current: chain 'G' and resid 220 through 234 removed outlier: 7.818A pdb=" N ILE G 226 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR G 268 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY G 228 " --> pdb=" O THR G 266 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 261 through 268 current: chain 'G' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 307 through 319 current: chain 'G' and resid 331 through 338 Processing sheet with id=AB6, first strand: chain 'G' and resid 43 through 46 Processing sheet with id=AB7, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.782A pdb=" N LYS G 86 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 238 through 240 removed outlier: 3.842A pdb=" N GLY G 253 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 378 through 382 removed outlier: 3.612A pdb=" N GLU G 401 " --> pdb=" O THR G 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 389 through 391 removed outlier: 7.071A pdb=" N LEU G 390 " --> pdb=" O THR G 461 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR G 441 " --> pdb=" O THR G 417 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 395 through 396 Processing sheet with id=AC3, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 111 Processing sheet with id=AC5, first strand: chain 'I' and resid 25 through 28 removed outlier: 4.370A pdb=" N ILE I 11 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP I 144 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 71 current: chain 'I' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 119 through 122 current: chain 'I' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 173 current: chain 'I' and resid 220 through 224 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 220 through 224 current: chain 'I' and resid 261 through 268 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 261 through 268 current: chain 'I' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 307 through 319 current: chain 'I' and resid 331 through 338 Processing sheet with id=AC7, first strand: chain 'I' and resid 43 through 46 Processing sheet with id=AC8, first strand: chain 'I' and resid 79 through 80 Processing sheet with id=AC9, first strand: chain 'I' and resid 238 through 240 removed outlier: 3.514A pdb=" N GLY I 253 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 378 through 382 Processing sheet with id=AD2, first strand: chain 'I' and resid 389 through 390 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 389 through 390 current: chain 'I' and resid 440 through 446 removed outlier: 3.943A pdb=" N ALA I 444 " --> pdb=" O GLY I 454 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY I 454 " --> pdb=" O ALA I 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 395 through 397 411 hydrogen bonds defined for protein. 1125 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: 2.39 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6087 1.34 - 1.46: 3797 1.46 - 1.58: 8602 1.58 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 18609 Sorted by residual: bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET I 1 " pdb=" CA MET I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 18604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 23775 1.02 - 2.05: 1282 2.05 - 3.07: 134 3.07 - 4.09: 92 4.09 - 5.12: 19 Bond angle restraints: 25302 Sorted by residual: angle pdb=" N ASN G 368 " pdb=" CA ASN G 368 " pdb=" C ASN G 368 " ideal model delta sigma weight residual 114.56 110.96 3.60 1.27e+00 6.20e-01 8.04e+00 angle pdb=" CA GLU I 194 " pdb=" CB GLU I 194 " pdb=" CG GLU I 194 " ideal model delta sigma weight residual 114.10 119.05 -4.95 2.00e+00 2.50e-01 6.13e+00 angle pdb=" CB GLU I 194 " pdb=" CG GLU I 194 " pdb=" CD GLU I 194 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.70e+00 3.46e-01 4.55e+00 angle pdb=" N GLY I 229 " pdb=" CA GLY I 229 " pdb=" C GLY I 229 " ideal model delta sigma weight residual 110.38 113.50 -3.12 1.48e+00 4.57e-01 4.45e+00 angle pdb=" CA ASN G 368 " pdb=" C ASN G 368 " pdb=" N GLY G 369 " ideal model delta sigma weight residual 119.26 116.91 2.35 1.14e+00 7.69e-01 4.25e+00 ... (remaining 25297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9669 17.97 - 35.93: 1171 35.93 - 53.90: 291 53.90 - 71.87: 63 71.87 - 89.84: 17 Dihedral angle restraints: 11211 sinusoidal: 4404 harmonic: 6807 Sorted by residual: dihedral pdb=" CA ALA H 310 " pdb=" C ALA H 310 " pdb=" N ILE H 311 " pdb=" CA ILE H 311 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ILE I 226 " pdb=" C ILE I 226 " pdb=" N THR I 227 " pdb=" CA THR I 227 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE D 28 " pdb=" C PHE D 28 " pdb=" N ASN D 29 " pdb=" CA ASN D 29 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 11208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1873 0.033 - 0.065: 717 0.065 - 0.098: 176 0.098 - 0.131: 156 0.131 - 0.163: 12 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA ILE I 250 " pdb=" N ILE I 250 " pdb=" C ILE I 250 " pdb=" CB ILE I 250 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE I 177 " pdb=" N ILE I 177 " pdb=" C ILE I 177 " pdb=" CB ILE I 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE G 250 " pdb=" N ILE G 250 " pdb=" C ILE G 250 " pdb=" CB ILE G 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2931 not shown) Planarity restraints: 3282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 113 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO F 114 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 113 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 113 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO D 114 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " 0.018 5.00e-02 4.00e+02 ... (remaining 3279 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 296 2.54 - 3.13: 15757 3.13 - 3.72: 27998 3.72 - 4.31: 38317 4.31 - 4.90: 64941 Nonbonded interactions: 147309 Sorted by model distance: nonbonded pdb=" OG1 THR H 413 " pdb=" OG1 THR H 445 " model vdw 1.950 3.040 nonbonded pdb=" OG1 THR G 413 " pdb=" OG1 THR G 445 " model vdw 1.989 3.040 nonbonded pdb=" OG1 THR H 380 " pdb=" OE2 GLU H 401 " model vdw 1.996 3.040 nonbonded pdb=" OG SER I 14 " pdb=" OG1 THR I 25 " model vdw 2.017 3.040 nonbonded pdb=" NH2 ARG E 14 " pdb=" O VAL E 100 " model vdw 2.069 3.120 ... (remaining 147304 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 159) selection = chain 'B' selection = (chain 'C' and resid 1 through 159) selection = chain 'D' selection = (chain 'E' and resid 1 through 159) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 0.034 18609 Z= 0.203 Angle : 0.554 5.118 25302 Z= 0.303 Chirality : 0.043 0.163 2934 Planarity : 0.003 0.039 3282 Dihedral : 16.797 89.836 6843 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.61 % Favored : 93.26 % Rotamer: Outliers : 0.15 % Allowed : 25.43 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2331 helix: 1.21 (0.29), residues: 324 sheet: -0.16 (0.18), residues: 852 loop : -1.45 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 14 TYR 0.015 0.001 TYR G 92 PHE 0.009 0.001 PHE G 231 TRP 0.018 0.001 TRP I 144 HIS 0.003 0.001 HIS H 129 Details of bonding type rmsd covalent geometry : bond 0.00422 (18609) covalent geometry : angle 0.55355 (25302) hydrogen bonds : bond 0.21735 ( 411) hydrogen bonds : angle 8.44644 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 682 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.5722 (ptp) cc_final: 0.5110 (mpp) REVERT: C 96 ASP cc_start: 0.5121 (OUTLIER) cc_final: 0.4730 (t0) REVERT: C 99 THR cc_start: 0.7302 (p) cc_final: 0.6522 (p) REVERT: C 102 ASP cc_start: 0.7821 (m-30) cc_final: 0.7460 (m-30) REVERT: D 16 SER cc_start: 0.7814 (m) cc_final: 0.7337 (p) REVERT: D 34 ASN cc_start: 0.6970 (t0) cc_final: 0.6590 (p0) REVERT: D 128 ILE cc_start: 0.7967 (mt) cc_final: 0.7650 (tp) REVERT: D 159 LEU cc_start: 0.5331 (mt) cc_final: 0.4526 (pp) REVERT: H 191 ILE cc_start: 0.6578 (pt) cc_final: 0.6222 (pt) REVERT: H 210 ILE cc_start: 0.7184 (mt) cc_final: 0.6974 (mt) REVERT: H 224 ILE cc_start: 0.8124 (mm) cc_final: 0.7829 (mp) REVERT: H 226 ILE cc_start: 0.7409 (mt) cc_final: 0.7153 (mt) REVERT: H 236 ASN cc_start: 0.5396 (m-40) cc_final: 0.3485 (m110) REVERT: A 11 MET cc_start: 0.9059 (tpp) cc_final: 0.8695 (ttt) REVERT: A 107 LEU cc_start: 0.8065 (tp) cc_final: 0.7801 (tp) REVERT: B 69 TRP cc_start: 0.7452 (m100) cc_final: 0.7167 (m100) REVERT: B 153 GLN cc_start: 0.8337 (tt0) cc_final: 0.7871 (tt0) REVERT: G 47 VAL cc_start: 0.8007 (m) cc_final: 0.7746 (p) REVERT: G 73 SER cc_start: 0.7676 (m) cc_final: 0.7425 (t) REVERT: G 122 ASN cc_start: 0.7843 (t0) cc_final: 0.7077 (t0) REVERT: G 144 TRP cc_start: 0.7585 (m100) cc_final: 0.7284 (m100) REVERT: G 177 ILE cc_start: 0.6812 (mp) cc_final: 0.6538 (mp) REVERT: G 213 ILE cc_start: 0.8155 (tt) cc_final: 0.7873 (tt) REVERT: G 264 SER cc_start: 0.7625 (p) cc_final: 0.6976 (t) REVERT: G 280 TYR cc_start: 0.7375 (t80) cc_final: 0.6659 (t80) REVERT: G 333 SER cc_start: 0.6109 (t) cc_final: 0.5838 (t) REVERT: G 353 PHE cc_start: 0.8059 (m-80) cc_final: 0.7832 (m-80) REVERT: G 398 MET cc_start: 0.4380 (tmm) cc_final: 0.3568 (tmm) REVERT: E 17 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7077 (mmmm) REVERT: E 63 LEU cc_start: 0.7139 (mm) cc_final: 0.6928 (mp) REVERT: E 72 LEU cc_start: 0.7029 (tt) cc_final: 0.6660 (tt) REVERT: F 27 TYR cc_start: 0.7589 (m-10) cc_final: 0.7098 (m-10) REVERT: F 58 GLU cc_start: 0.6517 (tt0) cc_final: 0.6093 (mt-10) REVERT: F 62 TYR cc_start: 0.6646 (m-10) cc_final: 0.6338 (m-10) REVERT: F 72 LEU cc_start: 0.8068 (tp) cc_final: 0.7482 (tp) REVERT: F 86 ILE cc_start: 0.8282 (tt) cc_final: 0.7944 (tt) REVERT: I 24 ASN cc_start: 0.6562 (p0) cc_final: 0.6294 (p0) REVERT: I 294 GLU cc_start: 0.3253 (pt0) cc_final: 0.2440 (pt0) REVERT: I 311 ILE cc_start: 0.5593 (mm) cc_final: 0.5277 (tp) REVERT: I 339 ILE cc_start: 0.8749 (pt) cc_final: 0.8146 (pt) outliers start: 3 outliers final: 1 residues processed: 682 average time/residue: 0.1188 time to fit residues: 123.5129 Evaluate side-chains 397 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 chunk 200 optimal weight: 6.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 HIS C 67 GLN ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 147 ASN H 66 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 ASN A 153 GLN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN G 48 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN I 153 ASN ** I 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083458 restraints weight = 46944.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085305 restraints weight = 26783.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.086567 restraints weight = 17996.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087394 restraints weight = 13570.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087982 restraints weight = 11178.064| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18609 Z= 0.159 Angle : 0.643 8.805 25302 Z= 0.337 Chirality : 0.047 0.179 2934 Planarity : 0.005 0.067 3282 Dihedral : 4.369 18.666 2529 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % Rotamer: Outliers : 0.15 % Allowed : 4.81 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.17), residues: 2331 helix: 0.81 (0.27), residues: 327 sheet: 0.12 (0.18), residues: 834 loop : -1.25 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 156 TYR 0.025 0.002 TYR E 152 PHE 0.037 0.002 PHE F 119 TRP 0.018 0.002 TRP C 69 HIS 0.008 0.002 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00362 (18609) covalent geometry : angle 0.64252 (25302) hydrogen bonds : bond 0.04400 ( 411) hydrogen bonds : angle 6.37131 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 552 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 THR cc_start: 0.7273 (p) cc_final: 0.6813 (p) REVERT: D 20 ASP cc_start: 0.7087 (m-30) cc_final: 0.6729 (m-30) REVERT: D 99 THR cc_start: 0.8103 (m) cc_final: 0.7441 (p) REVERT: D 159 LEU cc_start: 0.4648 (mt) cc_final: 0.4198 (pp) REVERT: H 24 ASN cc_start: 0.8026 (p0) cc_final: 0.7820 (p0) REVERT: H 277 MET cc_start: 0.6753 (mmm) cc_final: 0.6500 (mmm) REVERT: A 2 ASP cc_start: 0.6070 (t70) cc_final: 0.5859 (t70) REVERT: A 80 ASP cc_start: 0.6473 (t0) cc_final: 0.6236 (t0) REVERT: A 107 LEU cc_start: 0.8363 (tp) cc_final: 0.8061 (tp) REVERT: A 151 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7311 (mtp-110) REVERT: B 107 LEU cc_start: 0.7368 (mt) cc_final: 0.7128 (tt) REVERT: G 35 SER cc_start: 0.7468 (m) cc_final: 0.6907 (p) REVERT: G 213 ILE cc_start: 0.8259 (tt) cc_final: 0.8048 (tt) REVERT: G 280 TYR cc_start: 0.7320 (t80) cc_final: 0.6590 (t80) REVERT: G 287 LEU cc_start: 0.7590 (mt) cc_final: 0.7275 (mp) REVERT: G 353 PHE cc_start: 0.8305 (m-80) cc_final: 0.8032 (m-80) REVERT: E 1 MET cc_start: 0.6426 (pmm) cc_final: 0.4376 (tpt) REVERT: E 127 ILE cc_start: 0.8560 (mt) cc_final: 0.8341 (mt) REVERT: F 12 VAL cc_start: 0.7575 (t) cc_final: 0.7319 (t) REVERT: F 13 ASP cc_start: 0.8759 (m-30) cc_final: 0.8526 (m-30) REVERT: F 85 ASP cc_start: 0.7194 (t0) cc_final: 0.6901 (t70) REVERT: F 86 ILE cc_start: 0.7832 (tt) cc_final: 0.7561 (tt) REVERT: F 87 GLN cc_start: 0.8785 (mp10) cc_final: 0.8327 (mp10) REVERT: F 132 SER cc_start: 0.7342 (t) cc_final: 0.5497 (p) REVERT: F 143 LEU cc_start: 0.7643 (tp) cc_final: 0.7431 (tp) REVERT: F 145 GLU cc_start: 0.8025 (pm20) cc_final: 0.7451 (pm20) REVERT: I 398 MET cc_start: 0.4848 (pmm) cc_final: 0.4574 (pmm) outliers start: 3 outliers final: 0 residues processed: 554 average time/residue: 0.1008 time to fit residues: 88.2595 Evaluate side-chains 360 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 206 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 223 optimal weight: 40.0000 chunk 154 optimal weight: 8.9990 chunk 130 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 151 optimal weight: 50.0000 chunk 48 optimal weight: 9.9990 chunk 209 optimal weight: 0.0070 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 ASN A 153 GLN B 67 GLN B 89 GLN G 200 GLN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN I 235 ASN ** I 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085216 restraints weight = 47177.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087038 restraints weight = 26960.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088317 restraints weight = 18169.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.089082 restraints weight = 13700.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089710 restraints weight = 11387.494| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18609 Z= 0.128 Angle : 0.594 9.183 25302 Z= 0.308 Chirality : 0.045 0.163 2934 Planarity : 0.004 0.053 3282 Dihedral : 4.271 16.939 2529 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 0.20 % Allowed : 3.83 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2331 helix: 0.70 (0.27), residues: 327 sheet: 0.06 (0.18), residues: 849 loop : -1.15 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 151 TYR 0.018 0.002 TYR C 79 PHE 0.021 0.001 PHE F 28 TRP 0.024 0.002 TRP A 69 HIS 0.004 0.001 HIS D 3 Details of bonding type rmsd covalent geometry : bond 0.00290 (18609) covalent geometry : angle 0.59427 (25302) hydrogen bonds : bond 0.03893 ( 411) hydrogen bonds : angle 5.88973 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 481 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.6124 (ttm) cc_final: 0.5922 (ttm) REVERT: C 99 THR cc_start: 0.7704 (p) cc_final: 0.7146 (p) REVERT: D 20 ASP cc_start: 0.7127 (m-30) cc_final: 0.6786 (m-30) REVERT: D 72 LEU cc_start: 0.6675 (tp) cc_final: 0.6269 (tp) REVERT: D 99 THR cc_start: 0.8038 (m) cc_final: 0.7820 (p) REVERT: H 93 MET cc_start: 0.5947 (pmm) cc_final: 0.5072 (pmm) REVERT: A 1 MET cc_start: 0.6745 (pmm) cc_final: 0.4474 (tpp) REVERT: A 2 ASP cc_start: 0.6410 (t70) cc_final: 0.5831 (t70) REVERT: A 19 MET cc_start: 0.7813 (tpt) cc_final: 0.7496 (tpt) REVERT: A 55 ILE cc_start: 0.8127 (mm) cc_final: 0.7756 (mm) REVERT: A 80 ASP cc_start: 0.6454 (t0) cc_final: 0.6209 (t0) REVERT: A 107 LEU cc_start: 0.8448 (tp) cc_final: 0.8095 (tp) REVERT: B 1 MET cc_start: 0.3654 (mmm) cc_final: 0.3397 (mmm) REVERT: G 35 SER cc_start: 0.7198 (m) cc_final: 0.6897 (p) REVERT: G 213 ILE cc_start: 0.8382 (tt) cc_final: 0.8156 (tt) REVERT: G 280 TYR cc_start: 0.7547 (t80) cc_final: 0.6730 (t80) REVERT: G 287 LEU cc_start: 0.7743 (mt) cc_final: 0.7493 (mp) REVERT: G 295 ILE cc_start: 0.8431 (tt) cc_final: 0.8226 (tp) REVERT: G 362 ILE cc_start: 0.8322 (mt) cc_final: 0.8022 (mm) REVERT: G 370 ASP cc_start: 0.7074 (t70) cc_final: 0.6864 (t0) REVERT: E 1 MET cc_start: 0.6431 (pmm) cc_final: 0.4271 (tpt) REVERT: E 16 SER cc_start: 0.8345 (t) cc_final: 0.8141 (t) REVERT: F 1 MET cc_start: 0.5025 (tpp) cc_final: 0.4692 (tpt) REVERT: F 12 VAL cc_start: 0.7677 (t) cc_final: 0.7384 (t) REVERT: F 13 ASP cc_start: 0.8633 (m-30) cc_final: 0.8385 (m-30) REVERT: F 23 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8193 (mm-40) REVERT: F 55 ILE cc_start: 0.8405 (mp) cc_final: 0.8200 (mp) REVERT: F 85 ASP cc_start: 0.7180 (t0) cc_final: 0.6832 (t70) REVERT: F 132 SER cc_start: 0.7449 (t) cc_final: 0.6049 (p) REVERT: F 145 GLU cc_start: 0.7968 (pm20) cc_final: 0.7455 (pm20) REVERT: I 72 PHE cc_start: 0.8594 (p90) cc_final: 0.8345 (p90) outliers start: 4 outliers final: 0 residues processed: 482 average time/residue: 0.1071 time to fit residues: 82.0356 Evaluate side-chains 346 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 158 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 206 ASN H 320 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN G 153 ASN G 154 GLN G 174 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 3 HIS F 87 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN I 87 GLN I 409 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079911 restraints weight = 48524.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.081683 restraints weight = 29241.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082861 restraints weight = 20324.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083652 restraints weight = 15831.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.084172 restraints weight = 13301.980| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 18609 Z= 0.285 Angle : 0.865 12.852 25302 Z= 0.450 Chirality : 0.054 0.358 2934 Planarity : 0.006 0.084 3282 Dihedral : 5.474 35.549 2529 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 0.25 % Allowed : 6.58 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2331 helix: -0.17 (0.26), residues: 330 sheet: -0.35 (0.17), residues: 834 loop : -1.35 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 156 TYR 0.045 0.003 TYR C 109 PHE 0.026 0.003 PHE E 28 TRP 0.036 0.003 TRP I 70 HIS 0.007 0.002 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00658 (18609) covalent geometry : angle 0.86464 (25302) hydrogen bonds : bond 0.04903 ( 411) hydrogen bonds : angle 6.23077 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 402 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ASN cc_start: 0.7887 (t0) cc_final: 0.7366 (t0) REVERT: C 70 MET cc_start: 0.8062 (tpp) cc_final: 0.7645 (mmm) REVERT: D 1 MET cc_start: 0.5810 (tmm) cc_final: 0.5471 (tmm) REVERT: D 3 HIS cc_start: 0.6968 (m-70) cc_final: 0.6765 (m-70) REVERT: D 111 VAL cc_start: 0.7991 (t) cc_final: 0.7741 (t) REVERT: D 159 LEU cc_start: 0.5327 (mt) cc_final: 0.4691 (pp) REVERT: H 93 MET cc_start: 0.6731 (pmm) cc_final: 0.6417 (mtt) REVERT: H 120 MET cc_start: 0.8597 (ptp) cc_final: 0.7725 (ptp) REVERT: H 146 TYR cc_start: 0.8264 (p90) cc_final: 0.7781 (p90) REVERT: A 27 TYR cc_start: 0.7452 (m-80) cc_final: 0.6667 (m-10) REVERT: A 80 ASP cc_start: 0.6911 (t0) cc_final: 0.6630 (t0) REVERT: B 1 MET cc_start: 0.4730 (mmm) cc_final: 0.4470 (tpp) REVERT: B 18 GLN cc_start: 0.8248 (mp10) cc_final: 0.8022 (mp10) REVERT: B 23 GLN cc_start: 0.6854 (pp30) cc_final: 0.6591 (pp30) REVERT: B 126 MET cc_start: 0.7868 (mmm) cc_final: 0.7356 (mmm) REVERT: G 122 ASN cc_start: 0.8681 (t0) cc_final: 0.7906 (t0) REVERT: G 216 MET cc_start: 0.8418 (mmm) cc_final: 0.7999 (mmp) REVERT: G 277 MET cc_start: 0.8359 (mmm) cc_final: 0.8012 (tpp) REVERT: G 370 ASP cc_start: 0.7301 (t70) cc_final: 0.7061 (t0) REVERT: E 97 ILE cc_start: 0.8952 (pt) cc_final: 0.8743 (pt) REVERT: F 23 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8288 (mm-40) REVERT: F 70 MET cc_start: 0.6678 (tpp) cc_final: 0.6404 (tpt) REVERT: F 132 SER cc_start: 0.8100 (t) cc_final: 0.6819 (t) REVERT: I 122 ASN cc_start: 0.7596 (t0) cc_final: 0.6873 (m110) REVERT: I 146 TYR cc_start: 0.7333 (p90) cc_final: 0.6691 (p90) outliers start: 5 outliers final: 1 residues processed: 406 average time/residue: 0.1065 time to fit residues: 68.3796 Evaluate side-chains 263 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 195 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 89 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN A 18 GLN A 153 GLN G 409 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 87 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 GLN I 409 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.101339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.080064 restraints weight = 48044.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081897 restraints weight = 28087.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083168 restraints weight = 19474.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084040 restraints weight = 15101.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084546 restraints weight = 12638.182| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18609 Z= 0.156 Angle : 0.641 10.050 25302 Z= 0.335 Chirality : 0.047 0.188 2934 Planarity : 0.004 0.042 3282 Dihedral : 4.733 22.288 2529 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2331 helix: 0.16 (0.26), residues: 333 sheet: -0.45 (0.17), residues: 840 loop : -1.15 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 7 TYR 0.021 0.002 TYR E 109 PHE 0.016 0.002 PHE B 28 TRP 0.035 0.002 TRP I 144 HIS 0.008 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00357 (18609) covalent geometry : angle 0.64104 (25302) hydrogen bonds : bond 0.03715 ( 411) hydrogen bonds : angle 5.69128 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7447 (pmm) cc_final: 0.6972 (pmm) REVERT: C 30 ASN cc_start: 0.8006 (t0) cc_final: 0.7560 (t0) REVERT: D 1 MET cc_start: 0.5503 (tmm) cc_final: 0.5121 (tmm) REVERT: D 3 HIS cc_start: 0.7078 (m-70) cc_final: 0.6859 (m90) REVERT: H 31 GLN cc_start: 0.8919 (mm110) cc_final: 0.8588 (mm110) REVERT: H 146 TYR cc_start: 0.8427 (p90) cc_final: 0.7862 (p90) REVERT: A 1 MET cc_start: 0.7470 (pmm) cc_final: 0.6989 (pmm) REVERT: A 80 ASP cc_start: 0.6850 (t0) cc_final: 0.6615 (t0) REVERT: B 1 MET cc_start: 0.4253 (mmm) cc_final: 0.3734 (tpp) REVERT: B 18 GLN cc_start: 0.8422 (mp10) cc_final: 0.8204 (mp10) REVERT: B 23 GLN cc_start: 0.7059 (pp30) cc_final: 0.6749 (mt0) REVERT: B 126 MET cc_start: 0.8100 (mmm) cc_final: 0.7591 (mmm) REVERT: G 216 MET cc_start: 0.8537 (mmm) cc_final: 0.8237 (mmp) REVERT: G 277 MET cc_start: 0.8430 (mmm) cc_final: 0.8224 (tpp) REVERT: G 370 ASP cc_start: 0.7271 (t70) cc_final: 0.6877 (t0) REVERT: E 68 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8458 (tp40) REVERT: F 23 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8204 (mm-40) REVERT: I 125 ASP cc_start: 0.7246 (t70) cc_final: 0.6899 (t0) REVERT: I 156 GLU cc_start: 0.8045 (tp30) cc_final: 0.6721 (tt0) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1138 time to fit residues: 64.3200 Evaluate side-chains 248 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 89 GLN H 115 ASN H 175 GLN H 206 ASN H 236 ASN A 23 GLN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 106 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN F 87 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 GLN ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN I 409 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077418 restraints weight = 47863.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079147 restraints weight = 29101.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080358 restraints weight = 20629.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081169 restraints weight = 16102.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081658 restraints weight = 13553.728| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.8354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18609 Z= 0.193 Angle : 0.641 9.899 25302 Z= 0.337 Chirality : 0.047 0.185 2934 Planarity : 0.004 0.045 3282 Dihedral : 4.698 21.817 2529 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.17), residues: 2331 helix: 0.33 (0.26), residues: 333 sheet: -0.63 (0.17), residues: 876 loop : -1.20 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 56 TYR 0.026 0.002 TYR I 92 PHE 0.015 0.002 PHE F 42 TRP 0.037 0.002 TRP E 69 HIS 0.009 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00443 (18609) covalent geometry : angle 0.64095 (25302) hydrogen bonds : bond 0.03740 ( 411) hydrogen bonds : angle 5.42650 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: C 30 ASN cc_start: 0.8134 (t0) cc_final: 0.7700 (t0) REVERT: C 151 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.7943 (mtp-110) REVERT: D 1 MET cc_start: 0.5621 (tmm) cc_final: 0.5201 (tmm) REVERT: D 3 HIS cc_start: 0.7271 (m-70) cc_final: 0.7068 (m-70) REVERT: D 159 LEU cc_start: 0.5357 (mt) cc_final: 0.4273 (pp) REVERT: H 31 GLN cc_start: 0.8849 (mm110) cc_final: 0.8437 (mm110) REVERT: H 120 MET cc_start: 0.8838 (ptp) cc_final: 0.8153 (ptp) REVERT: A 101 ILE cc_start: 0.9335 (mm) cc_final: 0.9091 (mt) REVERT: B 1 MET cc_start: 0.4407 (mmm) cc_final: 0.4061 (mmm) REVERT: B 18 GLN cc_start: 0.8321 (mp10) cc_final: 0.7883 (mp10) REVERT: B 126 MET cc_start: 0.8182 (mmm) cc_final: 0.7864 (mmm) REVERT: G 1 MET cc_start: 0.3476 (ptt) cc_final: 0.2857 (ptt) REVERT: G 130 GLU cc_start: 0.8137 (pt0) cc_final: 0.7935 (pt0) REVERT: G 216 MET cc_start: 0.8628 (mmm) cc_final: 0.8183 (mmp) REVERT: G 277 MET cc_start: 0.8398 (mmm) cc_final: 0.8141 (tpp) REVERT: F 46 ARG cc_start: 0.7726 (mmp-170) cc_final: 0.7233 (mmp-170) REVERT: I 24 ASN cc_start: 0.8029 (p0) cc_final: 0.7685 (p0) REVERT: I 49 GLU cc_start: 0.3182 (tp30) cc_final: 0.2320 (tt0) REVERT: I 52 PRO cc_start: 0.6266 (Cg_exo) cc_final: 0.6009 (Cg_endo) REVERT: I 122 ASN cc_start: 0.7852 (t0) cc_final: 0.7183 (t0) REVERT: I 125 ASP cc_start: 0.7360 (t70) cc_final: 0.6981 (t0) REVERT: I 156 GLU cc_start: 0.8038 (tp30) cc_final: 0.6996 (tt0) REVERT: I 197 MET cc_start: 0.8280 (tpp) cc_final: 0.7923 (tpp) REVERT: I 277 MET cc_start: 0.8754 (mmm) cc_final: 0.8284 (mmt) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1238 time to fit residues: 63.6615 Evaluate side-chains 238 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 170 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 140 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 87 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 GLN I 26 GLN I 118 ASN I 135 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074072 restraints weight = 48775.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075818 restraints weight = 28963.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076954 restraints weight = 20335.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077821 restraints weight = 15976.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078343 restraints weight = 13424.906| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.9330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 18609 Z= 0.262 Angle : 0.706 8.051 25302 Z= 0.375 Chirality : 0.049 0.187 2934 Planarity : 0.005 0.055 3282 Dihedral : 5.010 24.193 2529 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.17), residues: 2331 helix: 0.06 (0.26), residues: 333 sheet: -0.61 (0.17), residues: 834 loop : -1.33 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 14 TYR 0.024 0.002 TYR I 280 PHE 0.022 0.002 PHE B 28 TRP 0.029 0.002 TRP E 69 HIS 0.007 0.002 HIS I 318 Details of bonding type rmsd covalent geometry : bond 0.00598 (18609) covalent geometry : angle 0.70563 (25302) hydrogen bonds : bond 0.04141 ( 411) hydrogen bonds : angle 5.58924 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7573 (pmm) cc_final: 0.7260 (pmm) REVERT: C 30 ASN cc_start: 0.8593 (t0) cc_final: 0.8049 (t0) REVERT: C 103 THR cc_start: 0.8155 (m) cc_final: 0.7950 (m) REVERT: D 1 MET cc_start: 0.5442 (tmm) cc_final: 0.5134 (tmm) REVERT: D 70 MET cc_start: 0.6701 (mmm) cc_final: 0.6175 (mmt) REVERT: D 145 GLU cc_start: 0.8161 (pm20) cc_final: 0.7797 (pm20) REVERT: H 120 MET cc_start: 0.8900 (ptp) cc_final: 0.8507 (ptp) REVERT: H 146 TYR cc_start: 0.8618 (p90) cc_final: 0.8044 (p90) REVERT: H 327 ASP cc_start: 0.7976 (t0) cc_final: 0.7457 (p0) REVERT: A 29 ASN cc_start: 0.8675 (m110) cc_final: 0.8408 (m110) REVERT: A 80 ASP cc_start: 0.6955 (t0) cc_final: 0.6737 (t0) REVERT: A 101 ILE cc_start: 0.9308 (mm) cc_final: 0.9035 (mt) REVERT: B 13 ASP cc_start: 0.8911 (m-30) cc_final: 0.8682 (m-30) REVERT: B 16 SER cc_start: 0.8728 (p) cc_final: 0.8489 (p) REVERT: B 18 GLN cc_start: 0.8626 (mp10) cc_final: 0.8052 (mp10) REVERT: B 26 GLU cc_start: 0.8038 (tt0) cc_final: 0.7784 (tt0) REVERT: B 27 TYR cc_start: 0.7118 (m-10) cc_final: 0.6823 (m-10) REVERT: G 1 MET cc_start: 0.3158 (ptt) cc_final: 0.2646 (ptt) REVERT: G 120 MET cc_start: 0.8753 (ptp) cc_final: 0.8502 (ptp) REVERT: G 216 MET cc_start: 0.8615 (mmm) cc_final: 0.8328 (mmp) REVERT: G 277 MET cc_start: 0.8702 (mmm) cc_final: 0.8300 (mmm) REVERT: F 11 MET cc_start: 0.9208 (tpp) cc_final: 0.8977 (tpp) REVERT: F 27 TYR cc_start: 0.8158 (m-10) cc_final: 0.7870 (m-10) REVERT: F 46 ARG cc_start: 0.7548 (mmp-170) cc_final: 0.7068 (mmp-170) REVERT: I 118 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8493 (p0) REVERT: I 125 ASP cc_start: 0.7892 (t70) cc_final: 0.7622 (t0) REVERT: I 156 GLU cc_start: 0.8181 (tp30) cc_final: 0.7160 (tt0) REVERT: I 197 MET cc_start: 0.8559 (tpp) cc_final: 0.8116 (tpp) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.1172 time to fit residues: 55.2579 Evaluate side-chains 218 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 103 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 195 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 113 HIS ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN G 200 GLN G 409 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 87 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN I 135 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074079 restraints weight = 47805.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075790 restraints weight = 28050.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076989 restraints weight = 19391.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077810 restraints weight = 14862.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078297 restraints weight = 12322.518| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.9510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18609 Z= 0.140 Angle : 0.596 8.700 25302 Z= 0.314 Chirality : 0.046 0.237 2934 Planarity : 0.004 0.045 3282 Dihedral : 4.672 20.389 2529 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 0.10 % Allowed : 1.08 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2331 helix: 0.33 (0.27), residues: 327 sheet: -0.62 (0.17), residues: 840 loop : -1.25 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 151 TYR 0.026 0.002 TYR I 92 PHE 0.029 0.002 PHE F 28 TRP 0.034 0.002 TRP C 69 HIS 0.006 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00326 (18609) covalent geometry : angle 0.59610 (25302) hydrogen bonds : bond 0.03554 ( 411) hydrogen bonds : angle 5.35627 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7591 (pmm) cc_final: 0.7229 (pmm) REVERT: C 30 ASN cc_start: 0.8594 (t0) cc_final: 0.8304 (t0) REVERT: D 1 MET cc_start: 0.5340 (tmm) cc_final: 0.5082 (tmm) REVERT: D 145 GLU cc_start: 0.7992 (pm20) cc_final: 0.7789 (pm20) REVERT: H 24 ASN cc_start: 0.8317 (p0) cc_final: 0.8095 (p0) REVERT: H 93 MET cc_start: 0.7421 (mtm) cc_final: 0.7194 (mtm) REVERT: H 120 MET cc_start: 0.8809 (ptp) cc_final: 0.8471 (ptp) REVERT: H 277 MET cc_start: 0.7702 (mmm) cc_final: 0.7414 (mmm) REVERT: H 316 GLN cc_start: 0.8554 (pm20) cc_final: 0.8339 (pm20) REVERT: H 327 ASP cc_start: 0.7911 (t0) cc_final: 0.7564 (p0) REVERT: A 29 ASN cc_start: 0.8737 (m110) cc_final: 0.8491 (m110) REVERT: A 101 ILE cc_start: 0.9203 (mm) cc_final: 0.8960 (mt) REVERT: B 18 GLN cc_start: 0.8618 (mp10) cc_final: 0.8041 (mp10) REVERT: B 27 TYR cc_start: 0.6808 (m-10) cc_final: 0.6484 (m-10) REVERT: B 130 SER cc_start: 0.9158 (p) cc_final: 0.8934 (p) REVERT: G 1 MET cc_start: 0.3651 (ptt) cc_final: 0.3189 (ptt) REVERT: G 53 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7794 (mmm160) REVERT: G 122 ASN cc_start: 0.8458 (t0) cc_final: 0.7950 (t0) REVERT: G 216 MET cc_start: 0.8459 (mmm) cc_final: 0.8153 (mmp) REVERT: G 277 MET cc_start: 0.8537 (mmm) cc_final: 0.7986 (mmm) REVERT: E 126 MET cc_start: 0.8620 (ttm) cc_final: 0.8261 (ttm) REVERT: F 27 TYR cc_start: 0.8010 (m-10) cc_final: 0.7767 (m-10) REVERT: F 35 VAL cc_start: 0.8047 (t) cc_final: 0.7634 (m) REVERT: F 70 MET cc_start: 0.6854 (mmm) cc_final: 0.6610 (mmt) REVERT: I 24 ASN cc_start: 0.8327 (p0) cc_final: 0.8093 (p0) REVERT: I 118 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8217 (p0) REVERT: I 122 ASN cc_start: 0.8264 (t0) cc_final: 0.7521 (t0) REVERT: I 125 ASP cc_start: 0.7713 (t70) cc_final: 0.7441 (t0) REVERT: I 156 GLU cc_start: 0.8052 (tp30) cc_final: 0.7213 (tt0) REVERT: I 408 ARG cc_start: 0.6822 (ptt180) cc_final: 0.6402 (ptt180) outliers start: 2 outliers final: 0 residues processed: 314 average time/residue: 0.1177 time to fit residues: 57.0523 Evaluate side-chains 227 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 89 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN G 409 ASN E 87 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN I 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.074385 restraints weight = 47797.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076135 restraints weight = 28038.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077320 restraints weight = 19249.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078193 restraints weight = 14735.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078704 restraints weight = 12114.659| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.9680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18609 Z= 0.146 Angle : 0.599 9.014 25302 Z= 0.314 Chirality : 0.045 0.170 2934 Planarity : 0.004 0.041 3282 Dihedral : 4.604 19.692 2529 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.17), residues: 2331 helix: 0.34 (0.27), residues: 327 sheet: -0.56 (0.18), residues: 789 loop : -1.20 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 151 TYR 0.021 0.001 TYR I 280 PHE 0.020 0.002 PHE F 28 TRP 0.049 0.002 TRP E 69 HIS 0.005 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00342 (18609) covalent geometry : angle 0.59943 (25302) hydrogen bonds : bond 0.03614 ( 411) hydrogen bonds : angle 5.29921 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7468 (pmm) cc_final: 0.7059 (pmm) REVERT: C 30 ASN cc_start: 0.8623 (t0) cc_final: 0.8073 (t0) REVERT: C 103 THR cc_start: 0.8181 (m) cc_final: 0.7972 (m) REVERT: D 1 MET cc_start: 0.5295 (tmm) cc_final: 0.4903 (tmm) REVERT: D 3 HIS cc_start: 0.7428 (m-70) cc_final: 0.7203 (m-70) REVERT: D 145 GLU cc_start: 0.8088 (pm20) cc_final: 0.7662 (pm20) REVERT: H 24 ASN cc_start: 0.8411 (p0) cc_final: 0.8147 (p0) REVERT: H 120 MET cc_start: 0.8699 (ptp) cc_final: 0.8269 (ptp) REVERT: H 133 MET cc_start: 0.8202 (tpt) cc_final: 0.7894 (mmm) REVERT: H 277 MET cc_start: 0.7777 (mmm) cc_final: 0.7443 (mmm) REVERT: H 327 ASP cc_start: 0.8008 (t0) cc_final: 0.7533 (p0) REVERT: A 101 ILE cc_start: 0.9236 (mm) cc_final: 0.8998 (mt) REVERT: B 1 MET cc_start: 0.4562 (tpp) cc_final: 0.4329 (tpp) REVERT: B 18 GLN cc_start: 0.8545 (mp10) cc_final: 0.7885 (mp10) REVERT: B 27 TYR cc_start: 0.6857 (m-10) cc_final: 0.6525 (m-10) REVERT: B 130 SER cc_start: 0.9140 (p) cc_final: 0.8903 (p) REVERT: B 145 GLU cc_start: 0.7692 (pp20) cc_final: 0.7378 (pp20) REVERT: G 1 MET cc_start: 0.3094 (ptt) cc_final: 0.2672 (ptt) REVERT: G 122 ASN cc_start: 0.8493 (t0) cc_final: 0.7965 (t0) REVERT: G 216 MET cc_start: 0.8579 (mmm) cc_final: 0.8307 (mmp) REVERT: G 277 MET cc_start: 0.8620 (mmm) cc_final: 0.8092 (mmm) REVERT: G 445 THR cc_start: 0.8277 (m) cc_final: 0.7982 (p) REVERT: E 126 MET cc_start: 0.8600 (ttm) cc_final: 0.8236 (ttm) REVERT: F 27 TYR cc_start: 0.8136 (m-10) cc_final: 0.7924 (m-10) REVERT: I 24 ASN cc_start: 0.8366 (p0) cc_final: 0.8131 (p0) REVERT: I 118 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8321 (p0) REVERT: I 122 ASN cc_start: 0.8260 (t0) cc_final: 0.7611 (t0) REVERT: I 125 ASP cc_start: 0.7708 (t70) cc_final: 0.7362 (t0) REVERT: I 156 GLU cc_start: 0.8107 (tp30) cc_final: 0.7352 (tt0) REVERT: I 197 MET cc_start: 0.8484 (tpt) cc_final: 0.8270 (tpp) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1114 time to fit residues: 53.9062 Evaluate side-chains 229 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 205 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.0050 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 219 optimal weight: 0.0770 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 89 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN G 409 ASN E 87 GLN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN I 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.074761 restraints weight = 47885.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076559 restraints weight = 27618.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077777 restraints weight = 18764.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078522 restraints weight = 14288.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079133 restraints weight = 11935.247| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.9810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18609 Z= 0.132 Angle : 0.585 8.995 25302 Z= 0.306 Chirality : 0.045 0.177 2934 Planarity : 0.004 0.045 3282 Dihedral : 4.485 21.271 2529 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2331 helix: 0.34 (0.27), residues: 327 sheet: -0.74 (0.17), residues: 852 loop : -1.15 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 151 TYR 0.026 0.001 TYR H 92 PHE 0.020 0.002 PHE F 28 TRP 0.022 0.002 TRP C 69 HIS 0.004 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00310 (18609) covalent geometry : angle 0.58513 (25302) hydrogen bonds : bond 0.03595 ( 411) hydrogen bonds : angle 5.26830 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7443 (pmm) cc_final: 0.7039 (pmm) REVERT: C 30 ASN cc_start: 0.8684 (t0) cc_final: 0.8430 (t0) REVERT: D 1 MET cc_start: 0.5246 (tmm) cc_final: 0.4944 (tmm) REVERT: D 3 HIS cc_start: 0.7483 (m-70) cc_final: 0.7231 (m-70) REVERT: D 70 MET cc_start: 0.6410 (mmm) cc_final: 0.6008 (mmt) REVERT: D 92 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8115 (mmtm) REVERT: D 145 GLU cc_start: 0.8039 (pm20) cc_final: 0.7742 (pm20) REVERT: H 120 MET cc_start: 0.8667 (ptp) cc_final: 0.8249 (ptp) REVERT: H 133 MET cc_start: 0.8247 (tpt) cc_final: 0.7647 (mmm) REVERT: H 277 MET cc_start: 0.7794 (mmm) cc_final: 0.7440 (mmm) REVERT: H 327 ASP cc_start: 0.8001 (t0) cc_final: 0.7545 (p0) REVERT: A 1 MET cc_start: 0.7706 (pmm) cc_final: 0.7021 (pmm) REVERT: A 101 ILE cc_start: 0.9284 (mm) cc_final: 0.9013 (mt) REVERT: B 1 MET cc_start: 0.4487 (tpp) cc_final: 0.4246 (tpt) REVERT: B 13 ASP cc_start: 0.8919 (m-30) cc_final: 0.8698 (m-30) REVERT: B 16 SER cc_start: 0.8713 (p) cc_final: 0.8504 (p) REVERT: B 18 GLN cc_start: 0.8506 (mp10) cc_final: 0.7878 (mp10) REVERT: B 27 TYR cc_start: 0.6875 (m-10) cc_final: 0.6513 (m-10) REVERT: B 130 SER cc_start: 0.9110 (p) cc_final: 0.8860 (p) REVERT: B 145 GLU cc_start: 0.7693 (pp20) cc_final: 0.7374 (pp20) REVERT: G 1 MET cc_start: 0.3091 (ptt) cc_final: 0.2738 (ptt) REVERT: G 122 ASN cc_start: 0.8424 (t0) cc_final: 0.7970 (t0) REVERT: G 277 MET cc_start: 0.8598 (mmm) cc_final: 0.8085 (mmm) REVERT: G 445 THR cc_start: 0.8265 (m) cc_final: 0.7965 (p) REVERT: E 126 MET cc_start: 0.8333 (ttm) cc_final: 0.8117 (ttm) REVERT: F 27 TYR cc_start: 0.8273 (m-10) cc_final: 0.7590 (m-10) REVERT: I 24 ASN cc_start: 0.8397 (p0) cc_final: 0.8158 (p0) REVERT: I 118 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8288 (p0) REVERT: I 122 ASN cc_start: 0.8260 (t0) cc_final: 0.7661 (t0) REVERT: I 125 ASP cc_start: 0.7638 (t70) cc_final: 0.7254 (t0) REVERT: I 156 GLU cc_start: 0.8183 (tp30) cc_final: 0.7436 (tt0) REVERT: I 197 MET cc_start: 0.8399 (tpt) cc_final: 0.8184 (tpp) REVERT: I 304 ASP cc_start: 0.8299 (m-30) cc_final: 0.7833 (p0) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.1093 time to fit residues: 54.5661 Evaluate side-chains 233 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 89 optimal weight: 5.9990 chunk 211 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN G 409 ASN E 87 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN I 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.075325 restraints weight = 47874.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.077012 restraints weight = 28264.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078096 restraints weight = 19468.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078915 restraints weight = 15031.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079385 restraints weight = 12421.375| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.9971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18609 Z= 0.137 Angle : 0.588 8.652 25302 Z= 0.308 Chirality : 0.045 0.161 2934 Planarity : 0.004 0.056 3282 Dihedral : 4.440 20.392 2529 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2331 helix: 0.33 (0.27), residues: 327 sheet: -0.60 (0.18), residues: 834 loop : -1.20 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 14 TYR 0.020 0.001 TYR I 280 PHE 0.028 0.002 PHE F 28 TRP 0.025 0.002 TRP I 144 HIS 0.005 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00323 (18609) covalent geometry : angle 0.58785 (25302) hydrogen bonds : bond 0.03567 ( 411) hydrogen bonds : angle 5.18955 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.37 seconds wall clock time: 46 minutes 4.72 seconds (2764.72 seconds total)