Starting phenix.real_space_refine on Wed Feb 4 01:59:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzh_66402/02_2026/9wzh_66402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzh_66402/02_2026/9wzh_66402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wzh_66402/02_2026/9wzh_66402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzh_66402/02_2026/9wzh_66402.map" model { file = "/net/cci-nas-00/data/ceres_data/9wzh_66402/02_2026/9wzh_66402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzh_66402/02_2026/9wzh_66402.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.015 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 24 5.16 5 C 5292 2.51 5 N 1440 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8256 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.21, per 1000 atoms: 0.27 Number of scatterers: 8256 At special positions: 0 Unit cell: (91.8, 90.1, 95.2, 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 24 16.00 O 1500 8.00 N 1440 7.00 C 5292 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: 0.82 Conformation dependent library (CDL) restraints added in 319.6 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 91.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.068A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.660A pdb=" N VAL A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.727A pdb=" N ALA A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.566A pdb=" N LYS A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.560A pdb=" N VAL A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.565A pdb=" N VAL B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 142 through 151 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.640A pdb=" N VAL C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 142 through 151 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.750A pdb=" N ALA D 168 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.711A pdb=" N VAL D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.827A pdb=" N ALA E 168 " --> pdb=" O PHE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 185 Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.836A pdb=" N ARG E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 165 through 169 removed outlier: 3.606A pdb=" N ALA F 168 " --> pdb=" O PHE F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 185 Processing helix chain 'F' and resid 185 through 194 removed outlier: 3.529A pdb=" N VAL F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 126 removed outlier: 3.578A pdb=" N VAL G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 137 Processing helix chain 'G' and resid 142 through 151 Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 165 through 169 removed outlier: 3.671A pdb=" N ALA G 168 " --> pdb=" O PHE G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 185 removed outlier: 3.536A pdb=" N LYS G 174 " --> pdb=" O ASN G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 194 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 126 removed outlier: 3.601A pdb=" N VAL H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 137 Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'H' and resid 154 through 164 Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 170 through 185 Processing helix chain 'H' and resid 185 through 194 removed outlier: 3.581A pdb=" N VAL H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 194 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 118 removed outlier: 3.678A pdb=" N GLN I 117 " --> pdb=" O HIS I 113 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS I 118 " --> pdb=" O PHE I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 118' Processing helix chain 'I' and resid 118 through 126 Processing helix chain 'I' and resid 129 through 137 Processing helix chain 'I' and resid 142 through 151 Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 165 through 169 removed outlier: 3.721A pdb=" N ALA I 168 " --> pdb=" O PHE I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 185 removed outlier: 3.518A pdb=" N LYS I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.069A pdb=" N VAL I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 126 Processing helix chain 'J' and resid 129 through 137 Processing helix chain 'J' and resid 142 through 151 Processing helix chain 'J' and resid 154 through 164 Processing helix chain 'J' and resid 165 through 169 removed outlier: 3.751A pdb=" N ALA J 168 " --> pdb=" O PHE J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 185 Processing helix chain 'J' and resid 185 through 194 removed outlier: 3.531A pdb=" N VAL J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 194 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 Processing helix chain 'K' and resid 129 through 137 Processing helix chain 'K' and resid 142 through 151 Processing helix chain 'K' and resid 154 through 164 Processing helix chain 'K' and resid 165 through 169 removed outlier: 3.943A pdb=" N ALA K 168 " --> pdb=" O PHE K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 185 Processing helix chain 'K' and resid 185 through 194 removed outlier: 3.561A pdb=" N VAL K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 126 removed outlier: 3.553A pdb=" N VAL L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'L' and resid 142 through 151 Processing helix chain 'L' and resid 154 through 164 Processing helix chain 'L' and resid 165 through 169 removed outlier: 3.983A pdb=" N ALA L 168 " --> pdb=" O PHE L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 185 Processing helix chain 'L' and resid 185 through 194 removed outlier: 3.563A pdb=" N VAL L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1467 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: 1.18 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2019 1.33 - 1.45: 1746 1.45 - 1.58: 4647 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 8448 Sorted by residual: bond pdb=" CA ASN K 128 " pdb=" CB ASN K 128 " ideal model delta sigma weight residual 1.528 1.549 -0.020 1.51e-02 4.39e+03 1.79e+00 bond pdb=" C THR I 166 " pdb=" N PRO I 167 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.65e+00 bond pdb=" CG GLU I 193 " pdb=" CD GLU I 193 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CD GLN B 147 " pdb=" OE1 GLN B 147 " ideal model delta sigma weight residual 1.231 1.212 0.019 1.90e-02 2.77e+03 1.00e+00 bond pdb=" CG ARG E 194 " pdb=" CD ARG E 194 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.72e-01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10979 1.76 - 3.53: 381 3.53 - 5.29: 79 5.29 - 7.05: 27 7.05 - 8.82: 6 Bond angle restraints: 11472 Sorted by residual: angle pdb=" N VAL D 140 " pdb=" CA VAL D 140 " pdb=" C VAL D 140 " ideal model delta sigma weight residual 113.71 109.45 4.26 9.50e-01 1.11e+00 2.01e+01 angle pdb=" N VAL J 140 " pdb=" CA VAL J 140 " pdb=" C VAL J 140 " ideal model delta sigma weight residual 113.71 109.76 3.95 9.50e-01 1.11e+00 1.73e+01 angle pdb=" N VAL I 140 " pdb=" CA VAL I 140 " pdb=" C VAL I 140 " ideal model delta sigma weight residual 113.53 109.47 4.06 9.80e-01 1.04e+00 1.71e+01 angle pdb=" N VAL F 140 " pdb=" CA VAL F 140 " pdb=" C VAL F 140 " ideal model delta sigma weight residual 113.71 109.84 3.87 9.50e-01 1.11e+00 1.66e+01 angle pdb=" N VAL C 140 " pdb=" CA VAL C 140 " pdb=" C VAL C 140 " ideal model delta sigma weight residual 113.71 109.90 3.81 9.50e-01 1.11e+00 1.61e+01 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 4392 14.14 - 28.28: 468 28.28 - 42.43: 177 42.43 - 56.57: 23 56.57 - 70.71: 16 Dihedral angle restraints: 5076 sinusoidal: 2088 harmonic: 2988 Sorted by residual: dihedral pdb=" CA GLU B 152 " pdb=" C GLU B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual -180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN G 117 " pdb=" C GLN G 117 " pdb=" N HIS G 118 " pdb=" CA HIS G 118 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU I 192 " pdb=" C LEU I 192 " pdb=" N GLU I 193 " pdb=" CA GLU I 193 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 715 0.030 - 0.060: 371 0.060 - 0.089: 113 0.089 - 0.119: 52 0.119 - 0.149: 21 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA PRO B 153 " pdb=" N PRO B 153 " pdb=" C PRO B 153 " pdb=" CB PRO B 153 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA THR F 166 " pdb=" N THR F 166 " pdb=" C THR F 166 " pdb=" CB THR F 166 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA THR H 166 " pdb=" N THR H 166 " pdb=" C THR H 166 " pdb=" CB THR H 166 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1269 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 193 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CD GLU E 193 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU E 193 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU E 193 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 144 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C GLU B 144 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU B 144 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN B 145 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 189 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C VAL H 189 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL H 189 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU H 190 " 0.009 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 108 2.64 - 3.20: 8096 3.20 - 3.77: 13421 3.77 - 4.33: 16488 4.33 - 4.90: 26343 Nonbonded interactions: 64456 Sorted by model distance: nonbonded pdb=" NH2 ARG A 160 " pdb=" OE1 GLU C 130 " model vdw 2.074 3.120 nonbonded pdb=" NH2 ARG D 160 " pdb=" OE1 GLU E 130 " model vdw 2.160 3.120 nonbonded pdb=" OE1 GLU F 130 " pdb=" NH2 ARG G 160 " model vdw 2.174 3.120 nonbonded pdb=" OD2 ASP F 134 " pdb=" NH2 ARG G 160 " model vdw 2.175 3.120 nonbonded pdb=" NH1 ARG E 160 " pdb=" OE2 GLU I 144 " model vdw 2.176 3.120 ... (remaining 64451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.110 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.550 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 : 0.003 0.030 8448 Z= 0.151 Angle : 0.826 8.818 11472 Z= 0.433 Chirality : 0.043 0.149 1272 Planarity : 0.004 0.052 1452 Dihedral : 13.941 70.711 3108 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.29), residues: 972 helix: 1.56 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.63 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 194 TYR 0.020 0.001 TYR K 146 PHE 0.014 0.001 PHE L 163 TRP 0.016 0.001 TRP G 131 HIS 0.004 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8448) covalent geometry : angle 0.82569 (11472) hydrogen bonds : bond 0.15750 ( 504) hydrogen bonds : angle 5.15475 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 0.330 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: A 128 ASN cc_start: 0.8813 (t0) cc_final: 0.8292 (t0) REVERT: A 145 GLN cc_start: 0.9609 (mt0) cc_final: 0.9369 (mt0) REVERT: A 146 TYR cc_start: 0.9306 (t80) cc_final: 0.8877 (t80) REVERT: A 150 ARG cc_start: 0.8866 (ttt90) cc_final: 0.8471 (tpp80) REVERT: A 179 GLN cc_start: 0.9688 (tp40) cc_final: 0.9450 (tm-30) REVERT: A 190 GLU cc_start: 0.9443 (tp30) cc_final: 0.9165 (tp30) REVERT: B 114 PHE cc_start: 0.8616 (t80) cc_final: 0.8264 (t80) REVERT: B 128 ASN cc_start: 0.8810 (t0) cc_final: 0.7683 (t0) REVERT: B 130 GLU cc_start: 0.9152 (pm20) cc_final: 0.8752 (pm20) REVERT: B 165 PHE cc_start: 0.9277 (m-10) cc_final: 0.9049 (m-10) REVERT: B 193 GLU cc_start: 0.8911 (pp20) cc_final: 0.8581 (pp20) REVERT: C 145 GLN cc_start: 0.9590 (mt0) cc_final: 0.9320 (mm-40) REVERT: C 165 PHE cc_start: 0.9298 (m-80) cc_final: 0.8782 (m-80) REVERT: C 175 ASP cc_start: 0.9174 (m-30) cc_final: 0.8974 (m-30) REVERT: C 179 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9251 (tm-30) REVERT: C 183 GLU cc_start: 0.9571 (tm-30) cc_final: 0.9253 (pp20) REVERT: C 190 GLU cc_start: 0.9587 (tp30) cc_final: 0.9283 (tp30) REVERT: D 128 ASN cc_start: 0.9087 (t0) cc_final: 0.8756 (t0) REVERT: D 134 ASP cc_start: 0.8562 (m-30) cc_final: 0.8180 (m-30) REVERT: D 145 GLN cc_start: 0.9257 (mt0) cc_final: 0.8880 (mt0) REVERT: D 147 GLN cc_start: 0.9045 (mp10) cc_final: 0.8710 (mp10) REVERT: D 169 TRP cc_start: 0.9485 (m-10) cc_final: 0.9257 (m-10) REVERT: D 173 CYS cc_start: 0.9129 (t) cc_final: 0.8869 (t) REVERT: D 179 GLN cc_start: 0.9436 (tm-30) cc_final: 0.9060 (tm-30) REVERT: D 183 GLU cc_start: 0.9299 (tm-30) cc_final: 0.9040 (pp20) REVERT: D 193 GLU cc_start: 0.8952 (pp20) cc_final: 0.8687 (pp20) REVERT: E 116 ASP cc_start: 0.9390 (t70) cc_final: 0.9187 (t70) REVERT: E 134 ASP cc_start: 0.8474 (m-30) cc_final: 0.8155 (m-30) REVERT: E 139 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9090 (mtmm) REVERT: E 179 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9186 (tm-30) REVERT: E 183 GLU cc_start: 0.9470 (tp30) cc_final: 0.9253 (tp30) REVERT: E 190 GLU cc_start: 0.9610 (tp30) cc_final: 0.8876 (tp30) REVERT: F 114 PHE cc_start: 0.9049 (t80) cc_final: 0.8757 (t80) REVERT: F 131 TRP cc_start: 0.8854 (t60) cc_final: 0.8451 (t60) REVERT: F 134 ASP cc_start: 0.8537 (m-30) cc_final: 0.8240 (m-30) REVERT: F 139 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8578 (mtmm) REVERT: F 143 ASP cc_start: 0.9626 (p0) cc_final: 0.9273 (p0) REVERT: F 147 GLN cc_start: 0.9338 (mp10) cc_final: 0.8952 (mp10) REVERT: F 175 ASP cc_start: 0.9102 (m-30) cc_final: 0.8881 (m-30) REVERT: F 183 GLU cc_start: 0.9395 (tp30) cc_final: 0.9178 (tp30) REVERT: F 190 GLU cc_start: 0.9451 (tp30) cc_final: 0.9249 (tm-30) REVERT: F 191 ASP cc_start: 0.9348 (t0) cc_final: 0.9094 (t0) REVERT: G 143 ASP cc_start: 0.9392 (t70) cc_final: 0.9190 (t70) REVERT: G 145 GLN cc_start: 0.9653 (mt0) cc_final: 0.9424 (mt0) REVERT: G 147 GLN cc_start: 0.9678 (mm-40) cc_final: 0.9407 (mm-40) REVERT: G 190 GLU cc_start: 0.9360 (tp30) cc_final: 0.8512 (tp30) REVERT: G 193 GLU cc_start: 0.8714 (pp20) cc_final: 0.7892 (pp20) REVERT: H 114 PHE cc_start: 0.9011 (t80) cc_final: 0.8811 (t80) REVERT: H 134 ASP cc_start: 0.8760 (m-30) cc_final: 0.8542 (m-30) REVERT: H 158 LYS cc_start: 0.9195 (mttp) cc_final: 0.8995 (mttp) REVERT: H 190 GLU cc_start: 0.9305 (tp30) cc_final: 0.9032 (tp30) REVERT: I 128 ASN cc_start: 0.9280 (t0) cc_final: 0.9051 (t0) REVERT: I 134 ASP cc_start: 0.8463 (m-30) cc_final: 0.8137 (m-30) REVERT: I 179 GLN cc_start: 0.9387 (tm-30) cc_final: 0.9141 (tm-30) REVERT: I 183 GLU cc_start: 0.9332 (tm-30) cc_final: 0.9109 (tm-30) REVERT: J 128 ASN cc_start: 0.8851 (t0) cc_final: 0.8158 (t0) REVERT: J 165 PHE cc_start: 0.9637 (m-10) cc_final: 0.9412 (m-10) REVERT: J 190 GLU cc_start: 0.9454 (tp30) cc_final: 0.8652 (tp30) REVERT: J 193 GLU cc_start: 0.8650 (pp20) cc_final: 0.7698 (pp20) REVERT: K 114 PHE cc_start: 0.9056 (t80) cc_final: 0.8856 (t80) REVERT: K 117 GLN cc_start: 0.9467 (tm-30) cc_final: 0.9263 (tm-30) REVERT: K 134 ASP cc_start: 0.8661 (m-30) cc_final: 0.8341 (m-30) REVERT: K 145 GLN cc_start: 0.9224 (tt0) cc_final: 0.9010 (mt0) REVERT: K 183 GLU cc_start: 0.9431 (tp30) cc_final: 0.9215 (tm-30) REVERT: K 190 GLU cc_start: 0.9232 (tp30) cc_final: 0.8611 (tp30) REVERT: K 193 GLU cc_start: 0.8519 (pp20) cc_final: 0.8179 (pp20) REVERT: L 134 ASP cc_start: 0.8477 (m-30) cc_final: 0.8199 (m-30) REVERT: L 146 TYR cc_start: 0.9367 (t80) cc_final: 0.9118 (t80) REVERT: L 150 ARG cc_start: 0.9368 (mmm-85) cc_final: 0.9050 (tpp80) REVERT: L 164 SER cc_start: 0.9593 (p) cc_final: 0.9050 (p) REVERT: L 190 GLU cc_start: 0.9412 (tp30) cc_final: 0.8790 (tp30) REVERT: L 193 GLU cc_start: 0.8437 (pp20) cc_final: 0.8221 (pp20) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1088 time to fit residues: 75.5269 Evaluate side-chains 452 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 145 GLN I 145 GLN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.060275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.049814 restraints weight = 30045.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.052003 restraints weight = 16429.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.053568 restraints weight = 10599.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.054707 restraints weight = 7465.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.055555 restraints weight = 5580.238| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8448 Z= 0.130 Angle : 0.645 6.290 11472 Z= 0.323 Chirality : 0.041 0.142 1272 Planarity : 0.005 0.037 1452 Dihedral : 3.906 15.526 1092 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.29), residues: 972 helix: 1.60 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.70 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 160 TYR 0.015 0.001 TYR B 146 PHE 0.012 0.002 PHE C 114 TRP 0.017 0.001 TRP C 131 HIS 0.003 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8448) covalent geometry : angle 0.64508 (11472) hydrogen bonds : bond 0.02950 ( 504) hydrogen bonds : angle 3.74001 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 PHE cc_start: 0.8722 (t80) cc_final: 0.8480 (t80) REVERT: A 130 GLU cc_start: 0.7915 (tt0) cc_final: 0.7374 (tt0) REVERT: A 134 ASP cc_start: 0.8997 (m-30) cc_final: 0.8549 (m-30) REVERT: A 145 GLN cc_start: 0.9599 (mt0) cc_final: 0.9372 (mt0) REVERT: A 160 ARG cc_start: 0.9401 (mtt180) cc_final: 0.9197 (mtt180) REVERT: A 179 GLN cc_start: 0.9716 (tp40) cc_final: 0.9432 (tm-30) REVERT: A 190 GLU cc_start: 0.9350 (tp30) cc_final: 0.9037 (tp30) REVERT: A 193 GLU cc_start: 0.8685 (pp20) cc_final: 0.8447 (pp20) REVERT: B 114 PHE cc_start: 0.8649 (t80) cc_final: 0.8367 (t80) REVERT: B 117 GLN cc_start: 0.9558 (tm-30) cc_final: 0.9342 (tm-30) REVERT: B 128 ASN cc_start: 0.8802 (t0) cc_final: 0.7487 (t0) REVERT: B 130 GLU cc_start: 0.9082 (pm20) cc_final: 0.8719 (pm20) REVERT: B 165 PHE cc_start: 0.9315 (m-10) cc_final: 0.9086 (m-10) REVERT: B 175 ASP cc_start: 0.9152 (m-30) cc_final: 0.8948 (m-30) REVERT: C 114 PHE cc_start: 0.8805 (t80) cc_final: 0.8411 (t80) REVERT: C 130 GLU cc_start: 0.8715 (pm20) cc_final: 0.8081 (pm20) REVERT: C 134 ASP cc_start: 0.8932 (m-30) cc_final: 0.8320 (m-30) REVERT: C 145 GLN cc_start: 0.9571 (mt0) cc_final: 0.9239 (mm110) REVERT: C 150 ARG cc_start: 0.9630 (mmm-85) cc_final: 0.9418 (mmm-85) REVERT: C 165 PHE cc_start: 0.9285 (m-80) cc_final: 0.8786 (m-80) REVERT: C 174 LYS cc_start: 0.9514 (mtmm) cc_final: 0.9240 (mtmm) REVERT: C 179 GLN cc_start: 0.9553 (tm-30) cc_final: 0.9278 (tm-30) REVERT: C 190 GLU cc_start: 0.9430 (tp30) cc_final: 0.8862 (tm-30) REVERT: D 114 PHE cc_start: 0.8773 (t80) cc_final: 0.8336 (t80) REVERT: D 128 ASN cc_start: 0.9037 (t0) cc_final: 0.8787 (t0) REVERT: D 134 ASP cc_start: 0.8602 (m-30) cc_final: 0.8251 (m-30) REVERT: D 145 GLN cc_start: 0.9349 (mt0) cc_final: 0.9100 (mt0) REVERT: D 158 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8375 (mtmm) REVERT: D 169 TRP cc_start: 0.9324 (m-10) cc_final: 0.9097 (m-10) REVERT: D 173 CYS cc_start: 0.9317 (t) cc_final: 0.9109 (t) REVERT: D 179 GLN cc_start: 0.9491 (tm-30) cc_final: 0.9197 (tm-30) REVERT: D 184 SER cc_start: 0.9068 (t) cc_final: 0.8687 (t) REVERT: D 193 GLU cc_start: 0.8945 (pp20) cc_final: 0.8484 (pp20) REVERT: E 114 PHE cc_start: 0.8872 (t80) cc_final: 0.8579 (t80) REVERT: E 134 ASP cc_start: 0.8845 (m-30) cc_final: 0.8580 (m-30) REVERT: E 139 LYS cc_start: 0.9448 (mtmm) cc_final: 0.9219 (mtmm) REVERT: E 169 TRP cc_start: 0.9372 (m-10) cc_final: 0.9017 (m-10) REVERT: E 179 GLN cc_start: 0.9417 (tm-30) cc_final: 0.9215 (tm-30) REVERT: F 114 PHE cc_start: 0.8808 (t80) cc_final: 0.8462 (t80) REVERT: F 134 ASP cc_start: 0.8897 (m-30) cc_final: 0.8668 (m-30) REVERT: F 143 ASP cc_start: 0.9590 (p0) cc_final: 0.9385 (p0) REVERT: F 191 ASP cc_start: 0.9281 (t0) cc_final: 0.8929 (t0) REVERT: G 130 GLU cc_start: 0.8019 (pm20) cc_final: 0.7760 (pm20) REVERT: G 179 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9240 (tm-30) REVERT: G 190 GLU cc_start: 0.9233 (tp30) cc_final: 0.8601 (tm-30) REVERT: H 114 PHE cc_start: 0.8716 (t80) cc_final: 0.8400 (t80) REVERT: H 117 GLN cc_start: 0.9480 (tm-30) cc_final: 0.9280 (tm-30) REVERT: H 134 ASP cc_start: 0.8952 (m-30) cc_final: 0.8690 (m-30) REVERT: H 158 LYS cc_start: 0.9190 (mttp) cc_final: 0.8985 (mttp) REVERT: H 174 LYS cc_start: 0.9382 (mttp) cc_final: 0.9090 (mtmm) REVERT: H 190 GLU cc_start: 0.9247 (tp30) cc_final: 0.8599 (tp30) REVERT: I 126 VAL cc_start: 0.9390 (t) cc_final: 0.9186 (p) REVERT: I 134 ASP cc_start: 0.8441 (m-30) cc_final: 0.8106 (m-30) REVERT: I 143 ASP cc_start: 0.8562 (t70) cc_final: 0.7589 (t70) REVERT: I 147 GLN cc_start: 0.9584 (mm-40) cc_final: 0.8958 (mp10) REVERT: I 158 LYS cc_start: 0.9010 (mttp) cc_final: 0.8767 (mttp) REVERT: I 179 GLN cc_start: 0.9426 (tm-30) cc_final: 0.9130 (tm-30) REVERT: I 183 GLU cc_start: 0.9255 (tm-30) cc_final: 0.9028 (tm-30) REVERT: I 190 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9060 (tp30) REVERT: I 193 GLU cc_start: 0.8891 (pm20) cc_final: 0.8573 (pm20) REVERT: J 128 ASN cc_start: 0.8817 (t0) cc_final: 0.8309 (t0) REVERT: J 129 VAL cc_start: 0.9366 (p) cc_final: 0.9105 (p) REVERT: J 134 ASP cc_start: 0.8730 (m-30) cc_final: 0.7898 (m-30) REVERT: J 190 GLU cc_start: 0.9349 (tp30) cc_final: 0.8524 (tp30) REVERT: J 193 GLU cc_start: 0.8612 (pp20) cc_final: 0.7708 (pp20) REVERT: K 114 PHE cc_start: 0.8758 (t80) cc_final: 0.8440 (t80) REVERT: K 117 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9172 (tm-30) REVERT: K 134 ASP cc_start: 0.8573 (m-30) cc_final: 0.8255 (m-30) REVERT: K 139 LYS cc_start: 0.9344 (mtmm) cc_final: 0.9050 (mtmm) REVERT: K 144 GLU cc_start: 0.9292 (tt0) cc_final: 0.8799 (tt0) REVERT: K 145 GLN cc_start: 0.9289 (tt0) cc_final: 0.9053 (mm110) REVERT: K 165 PHE cc_start: 0.9168 (m-10) cc_final: 0.8936 (m-10) REVERT: K 190 GLU cc_start: 0.9106 (tp30) cc_final: 0.8593 (tp30) REVERT: K 193 GLU cc_start: 0.8581 (pp20) cc_final: 0.8174 (pp20) REVERT: L 134 ASP cc_start: 0.8816 (m-30) cc_final: 0.8551 (m-30) REVERT: L 146 TYR cc_start: 0.9416 (t80) cc_final: 0.9163 (t80) REVERT: L 150 ARG cc_start: 0.9427 (mmm-85) cc_final: 0.9196 (tpp80) REVERT: L 174 LYS cc_start: 0.9567 (mttt) cc_final: 0.9148 (mttp) REVERT: L 190 GLU cc_start: 0.9211 (tp30) cc_final: 0.8751 (tp30) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.1029 time to fit residues: 71.2856 Evaluate side-chains 434 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 145 GLN I 145 GLN L 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.061232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.051867 restraints weight = 30177.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.053908 restraints weight = 16845.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.055335 restraints weight = 10935.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.056373 restraints weight = 7736.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.057138 restraints weight = 5789.713| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8448 Z= 0.119 Angle : 0.647 6.294 11472 Z= 0.312 Chirality : 0.040 0.158 1272 Planarity : 0.004 0.040 1452 Dihedral : 3.740 14.349 1092 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.29), residues: 972 helix: 1.51 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.72 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 194 TYR 0.009 0.001 TYR F 187 PHE 0.021 0.002 PHE F 163 TRP 0.025 0.001 TRP L 131 HIS 0.005 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8448) covalent geometry : angle 0.64678 (11472) hydrogen bonds : bond 0.02541 ( 504) hydrogen bonds : angle 3.49423 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 542 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8954 (m-30) cc_final: 0.8588 (m-30) REVERT: A 179 GLN cc_start: 0.9679 (tp40) cc_final: 0.9412 (tm-30) REVERT: A 190 GLU cc_start: 0.9183 (tp30) cc_final: 0.8878 (tp30) REVERT: A 193 GLU cc_start: 0.8660 (pp20) cc_final: 0.8408 (pp20) REVERT: B 114 PHE cc_start: 0.8653 (t80) cc_final: 0.8396 (t80) REVERT: B 128 ASN cc_start: 0.8819 (t0) cc_final: 0.7766 (t0) REVERT: B 130 GLU cc_start: 0.8980 (pm20) cc_final: 0.8702 (pm20) REVERT: B 165 PHE cc_start: 0.9285 (m-10) cc_final: 0.9027 (m-10) REVERT: B 175 ASP cc_start: 0.9120 (m-30) cc_final: 0.8887 (m-30) REVERT: B 179 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9302 (tm-30) REVERT: B 190 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8751 (tm-30) REVERT: B 191 ASP cc_start: 0.8977 (t0) cc_final: 0.8770 (t0) REVERT: C 114 PHE cc_start: 0.8864 (t80) cc_final: 0.8395 (t80) REVERT: C 117 GLN cc_start: 0.9513 (tm-30) cc_final: 0.9261 (tm-30) REVERT: C 128 ASN cc_start: 0.8533 (t0) cc_final: 0.7754 (t0) REVERT: C 130 GLU cc_start: 0.8558 (pm20) cc_final: 0.8047 (pm20) REVERT: C 131 TRP cc_start: 0.9227 (t-100) cc_final: 0.8953 (t60) REVERT: C 134 ASP cc_start: 0.8797 (m-30) cc_final: 0.8067 (m-30) REVERT: C 145 GLN cc_start: 0.9515 (mt0) cc_final: 0.9135 (mm110) REVERT: C 147 GLN cc_start: 0.9681 (mm-40) cc_final: 0.9413 (mm-40) REVERT: C 150 ARG cc_start: 0.9696 (mmm-85) cc_final: 0.9380 (mmm-85) REVERT: C 158 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8754 (mttp) REVERT: C 165 PHE cc_start: 0.9138 (m-80) cc_final: 0.8644 (m-80) REVERT: C 174 LYS cc_start: 0.9487 (mtmm) cc_final: 0.9216 (mtmm) REVERT: C 190 GLU cc_start: 0.9309 (tp30) cc_final: 0.8878 (tm-30) REVERT: D 114 PHE cc_start: 0.8538 (t80) cc_final: 0.8282 (t80) REVERT: D 117 GLN cc_start: 0.9461 (tp-100) cc_final: 0.9229 (tp-100) REVERT: D 134 ASP cc_start: 0.8560 (m-30) cc_final: 0.8258 (m-30) REVERT: D 139 LYS cc_start: 0.9276 (mtmm) cc_final: 0.8933 (mppt) REVERT: D 147 GLN cc_start: 0.9154 (mp10) cc_final: 0.8811 (mt0) REVERT: D 169 TRP cc_start: 0.9220 (m-10) cc_final: 0.8795 (m-10) REVERT: D 179 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9193 (tm-30) REVERT: D 193 GLU cc_start: 0.8805 (pp20) cc_final: 0.8361 (pp20) REVERT: E 114 PHE cc_start: 0.8934 (t80) cc_final: 0.8619 (t80) REVERT: E 117 GLN cc_start: 0.9274 (tm-30) cc_final: 0.9044 (tm-30) REVERT: E 130 GLU cc_start: 0.8397 (pm20) cc_final: 0.7870 (pm20) REVERT: E 134 ASP cc_start: 0.8900 (m-30) cc_final: 0.8561 (m-30) REVERT: E 139 LYS cc_start: 0.9410 (mtmm) cc_final: 0.9015 (mtmm) REVERT: E 143 ASP cc_start: 0.8011 (t0) cc_final: 0.7112 (t70) REVERT: E 144 GLU cc_start: 0.8430 (tt0) cc_final: 0.8211 (tt0) REVERT: E 147 GLN cc_start: 0.9503 (mm-40) cc_final: 0.8863 (mp10) REVERT: E 160 ARG cc_start: 0.9131 (mtm180) cc_final: 0.8756 (mtm180) REVERT: E 169 TRP cc_start: 0.9264 (m-10) cc_final: 0.8913 (m-10) REVERT: E 179 GLN cc_start: 0.9403 (tm-30) cc_final: 0.9164 (tm-30) REVERT: E 190 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9057 (tp30) REVERT: F 114 PHE cc_start: 0.8855 (t80) cc_final: 0.8605 (t80) REVERT: F 130 GLU cc_start: 0.8855 (pm20) cc_final: 0.8331 (pm20) REVERT: F 143 ASP cc_start: 0.9524 (p0) cc_final: 0.9168 (p0) REVERT: F 145 GLN cc_start: 0.9431 (mt0) cc_final: 0.8879 (mt0) REVERT: F 147 GLN cc_start: 0.9373 (mp10) cc_final: 0.8931 (mt0) REVERT: F 169 TRP cc_start: 0.9288 (m-10) cc_final: 0.9006 (m-10) REVERT: F 191 ASP cc_start: 0.9091 (t0) cc_final: 0.8889 (t0) REVERT: G 130 GLU cc_start: 0.8352 (pm20) cc_final: 0.8041 (pm20) REVERT: G 131 TRP cc_start: 0.8796 (t60) cc_final: 0.8357 (t60) REVERT: G 165 PHE cc_start: 0.9565 (m-10) cc_final: 0.9162 (m-80) REVERT: G 175 ASP cc_start: 0.9632 (t0) cc_final: 0.9424 (t0) REVERT: G 176 LEU cc_start: 0.9580 (tt) cc_final: 0.9368 (tt) REVERT: G 179 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9281 (tm-30) REVERT: H 114 PHE cc_start: 0.8787 (t80) cc_final: 0.8543 (t80) REVERT: H 130 GLU cc_start: 0.8592 (pm20) cc_final: 0.8259 (pm20) REVERT: H 134 ASP cc_start: 0.8880 (m-30) cc_final: 0.8124 (m-30) REVERT: H 158 LYS cc_start: 0.9299 (mttp) cc_final: 0.9060 (mttp) REVERT: H 173 CYS cc_start: 0.9608 (m) cc_final: 0.8847 (t) REVERT: H 174 LYS cc_start: 0.9474 (mttp) cc_final: 0.9138 (mtmm) REVERT: H 179 GLN cc_start: 0.9532 (tm-30) cc_final: 0.9302 (tm-30) REVERT: H 190 GLU cc_start: 0.9098 (tp30) cc_final: 0.8559 (tp30) REVERT: I 126 VAL cc_start: 0.9349 (t) cc_final: 0.9076 (p) REVERT: I 134 ASP cc_start: 0.8384 (m-30) cc_final: 0.8068 (m-30) REVERT: I 143 ASP cc_start: 0.8542 (t70) cc_final: 0.7648 (t70) REVERT: I 147 GLN cc_start: 0.9567 (mm-40) cc_final: 0.8930 (mt0) REVERT: I 179 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9130 (tm-30) REVERT: I 190 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8686 (tp30) REVERT: I 193 GLU cc_start: 0.8656 (pm20) cc_final: 0.8448 (pm20) REVERT: J 128 ASN cc_start: 0.8393 (t0) cc_final: 0.8154 (t0) REVERT: J 134 ASP cc_start: 0.8876 (m-30) cc_final: 0.7920 (m-30) REVERT: J 145 GLN cc_start: 0.9497 (mt0) cc_final: 0.9283 (mt0) REVERT: J 190 GLU cc_start: 0.9147 (tp30) cc_final: 0.8224 (tp30) REVERT: J 193 GLU cc_start: 0.8589 (pp20) cc_final: 0.7676 (pp20) REVERT: K 114 PHE cc_start: 0.8794 (t80) cc_final: 0.8586 (t80) REVERT: K 126 VAL cc_start: 0.9422 (t) cc_final: 0.9085 (p) REVERT: K 134 ASP cc_start: 0.8514 (m-30) cc_final: 0.8184 (m-30) REVERT: K 139 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9105 (mtmm) REVERT: K 154 THR cc_start: 0.8238 (p) cc_final: 0.7968 (p) REVERT: K 158 LYS cc_start: 0.9108 (mttp) cc_final: 0.8752 (mttp) REVERT: K 190 GLU cc_start: 0.8962 (tp30) cc_final: 0.8394 (tp30) REVERT: K 193 GLU cc_start: 0.8522 (pp20) cc_final: 0.8081 (pp20) REVERT: L 116 ASP cc_start: 0.9197 (t70) cc_final: 0.8990 (t0) REVERT: L 134 ASP cc_start: 0.8758 (m-30) cc_final: 0.8504 (m-30) REVERT: L 174 LYS cc_start: 0.9635 (mttt) cc_final: 0.9222 (mttp) REVERT: L 190 GLU cc_start: 0.9065 (tp30) cc_final: 0.8616 (tp30) outliers start: 1 outliers final: 0 residues processed: 542 average time/residue: 0.1019 time to fit residues: 73.4355 Evaluate side-chains 466 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN I 145 GLN K 145 GLN L 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.050030 restraints weight = 31788.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.052001 restraints weight = 17514.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.053382 restraints weight = 11328.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054383 restraints weight = 8014.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.055132 restraints weight = 5990.066| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8448 Z= 0.137 Angle : 0.649 6.223 11472 Z= 0.313 Chirality : 0.040 0.139 1272 Planarity : 0.004 0.040 1452 Dihedral : 3.842 16.775 1092 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.23 % Allowed : 2.48 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.29), residues: 972 helix: 1.51 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.75 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 194 TYR 0.017 0.001 TYR G 146 PHE 0.017 0.001 PHE K 165 TRP 0.025 0.001 TRP J 131 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8448) covalent geometry : angle 0.64894 (11472) hydrogen bonds : bond 0.02608 ( 504) hydrogen bonds : angle 3.65280 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 527 time to evaluate : 0.348 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: A 145 GLN cc_start: 0.9504 (mt0) cc_final: 0.9302 (mt0) REVERT: A 158 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8681 (mtmm) REVERT: A 160 ARG cc_start: 0.9439 (mtt180) cc_final: 0.9171 (mtt180) REVERT: A 179 GLN cc_start: 0.9713 (tp40) cc_final: 0.9435 (tm-30) REVERT: A 190 GLU cc_start: 0.9247 (tp30) cc_final: 0.8929 (tp30) REVERT: A 193 GLU cc_start: 0.8737 (pp20) cc_final: 0.8496 (pp20) REVERT: B 114 PHE cc_start: 0.8727 (t80) cc_final: 0.8481 (t80) REVERT: B 117 GLN cc_start: 0.9528 (tm-30) cc_final: 0.9309 (tm-30) REVERT: B 128 ASN cc_start: 0.8943 (t0) cc_final: 0.7875 (t0) REVERT: B 130 GLU cc_start: 0.8992 (pm20) cc_final: 0.8750 (pm20) REVERT: B 175 ASP cc_start: 0.9158 (m-30) cc_final: 0.8915 (m-30) REVERT: B 179 GLN cc_start: 0.9555 (tm-30) cc_final: 0.9339 (tm-30) REVERT: B 190 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8802 (tm-30) REVERT: B 191 ASP cc_start: 0.9056 (t0) cc_final: 0.8799 (t0) REVERT: C 114 PHE cc_start: 0.8899 (t80) cc_final: 0.8405 (t80) REVERT: C 130 GLU cc_start: 0.8637 (pm20) cc_final: 0.8106 (pm20) REVERT: C 131 TRP cc_start: 0.9360 (t-100) cc_final: 0.9001 (t60) REVERT: C 134 ASP cc_start: 0.8905 (m-30) cc_final: 0.8064 (m-30) REVERT: C 143 ASP cc_start: 0.9101 (t70) cc_final: 0.8865 (t0) REVERT: C 147 GLN cc_start: 0.9708 (mm-40) cc_final: 0.9395 (mm-40) REVERT: C 150 ARG cc_start: 0.9724 (mmm-85) cc_final: 0.9446 (mmm-85) REVERT: C 158 LYS cc_start: 0.9191 (mtmm) cc_final: 0.8925 (mtmm) REVERT: C 165 PHE cc_start: 0.9223 (m-80) cc_final: 0.8988 (m-80) REVERT: C 174 LYS cc_start: 0.9520 (mtmm) cc_final: 0.9183 (mtmm) REVERT: C 190 GLU cc_start: 0.9296 (tp30) cc_final: 0.8919 (tm-30) REVERT: D 117 GLN cc_start: 0.9481 (tp-100) cc_final: 0.9231 (tp-100) REVERT: D 134 ASP cc_start: 0.8624 (m-30) cc_final: 0.8285 (m-30) REVERT: D 158 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8588 (mttp) REVERT: D 169 TRP cc_start: 0.9273 (m-10) cc_final: 0.8832 (m-10) REVERT: D 179 GLN cc_start: 0.9517 (tm-30) cc_final: 0.9236 (tm-30) REVERT: D 184 SER cc_start: 0.9311 (t) cc_final: 0.9055 (t) REVERT: D 193 GLU cc_start: 0.8776 (pp20) cc_final: 0.8341 (pp20) REVERT: E 114 PHE cc_start: 0.9007 (t80) cc_final: 0.8665 (t80) REVERT: E 128 ASN cc_start: 0.8289 (t0) cc_final: 0.7198 (t0) REVERT: E 134 ASP cc_start: 0.9007 (m-30) cc_final: 0.8668 (m-30) REVERT: E 139 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9114 (mtmm) REVERT: E 147 GLN cc_start: 0.9564 (mm-40) cc_final: 0.9258 (mt0) REVERT: E 160 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8662 (mtm-85) REVERT: E 169 TRP cc_start: 0.9364 (m-10) cc_final: 0.8968 (m-10) REVERT: E 179 GLN cc_start: 0.9449 (tm-30) cc_final: 0.9223 (tm-30) REVERT: E 190 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9128 (tp30) REVERT: F 130 GLU cc_start: 0.8822 (pm20) cc_final: 0.8507 (pm20) REVERT: F 134 ASP cc_start: 0.8747 (m-30) cc_final: 0.8277 (m-30) REVERT: F 145 GLN cc_start: 0.9451 (mt0) cc_final: 0.8838 (mt0) REVERT: F 165 PHE cc_start: 0.9303 (m-80) cc_final: 0.9044 (m-80) REVERT: F 191 ASP cc_start: 0.9126 (t0) cc_final: 0.8865 (t0) REVERT: G 117 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9190 (tm-30) REVERT: G 130 GLU cc_start: 0.8261 (pm20) cc_final: 0.8047 (pm20) REVERT: G 158 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8883 (mtmm) REVERT: G 160 ARG cc_start: 0.9553 (mtt180) cc_final: 0.9226 (mtt180) REVERT: G 179 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9312 (tm-30) REVERT: G 190 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8707 (tm-30) REVERT: H 114 PHE cc_start: 0.8894 (t80) cc_final: 0.8610 (t80) REVERT: H 117 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9296 (tm-30) REVERT: H 130 GLU cc_start: 0.8814 (pm20) cc_final: 0.8393 (pm20) REVERT: H 134 ASP cc_start: 0.8970 (m-30) cc_final: 0.8286 (m-30) REVERT: H 154 THR cc_start: 0.8778 (p) cc_final: 0.8543 (p) REVERT: H 158 LYS cc_start: 0.9289 (mttp) cc_final: 0.9026 (mttp) REVERT: H 174 LYS cc_start: 0.9511 (mttp) cc_final: 0.9208 (mtmm) REVERT: H 179 GLN cc_start: 0.9554 (tm-30) cc_final: 0.9320 (tm-30) REVERT: H 190 GLU cc_start: 0.9075 (tp30) cc_final: 0.8672 (tp30) REVERT: I 134 ASP cc_start: 0.8503 (m-30) cc_final: 0.8139 (m-30) REVERT: I 143 ASP cc_start: 0.8560 (t70) cc_final: 0.7929 (t70) REVERT: I 147 GLN cc_start: 0.9588 (mm-40) cc_final: 0.9109 (mt0) REVERT: I 158 LYS cc_start: 0.9106 (mttp) cc_final: 0.8805 (mttp) REVERT: I 173 CYS cc_start: 0.9365 (m) cc_final: 0.8874 (t) REVERT: I 179 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9153 (tm-30) REVERT: I 190 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8881 (tp30) REVERT: J 128 ASN cc_start: 0.8875 (t0) cc_final: 0.8293 (t0) REVERT: J 134 ASP cc_start: 0.8898 (m-30) cc_final: 0.8545 (m-30) REVERT: J 143 ASP cc_start: 0.9105 (t70) cc_final: 0.8863 (t0) REVERT: J 158 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8583 (mttp) REVERT: J 160 ARG cc_start: 0.9540 (mtt180) cc_final: 0.9119 (mtt180) REVERT: J 165 PHE cc_start: 0.9504 (m-10) cc_final: 0.9227 (m-10) REVERT: J 169 TRP cc_start: 0.9331 (m-10) cc_final: 0.9005 (m-10) REVERT: J 174 LYS cc_start: 0.9433 (mttp) cc_final: 0.9006 (mtmm) REVERT: J 190 GLU cc_start: 0.9151 (tp30) cc_final: 0.8212 (tp30) REVERT: J 193 GLU cc_start: 0.8629 (pp20) cc_final: 0.7709 (pp20) REVERT: K 114 PHE cc_start: 0.8832 (t80) cc_final: 0.8595 (t80) REVERT: K 117 GLN cc_start: 0.9361 (tm-30) cc_final: 0.9116 (tm-30) REVERT: K 134 ASP cc_start: 0.8559 (m-30) cc_final: 0.8227 (m-30) REVERT: K 139 LYS cc_start: 0.9363 (mtmm) cc_final: 0.9079 (mtmm) REVERT: K 179 GLN cc_start: 0.9383 (tm-30) cc_final: 0.9142 (tm-30) REVERT: K 190 GLU cc_start: 0.9016 (tp30) cc_final: 0.8394 (tp30) REVERT: K 193 GLU cc_start: 0.8583 (pp20) cc_final: 0.8071 (pp20) REVERT: L 116 ASP cc_start: 0.9261 (t70) cc_final: 0.9004 (t0) REVERT: L 128 ASN cc_start: 0.8516 (t0) cc_final: 0.7735 (t0) REVERT: L 130 GLU cc_start: 0.8388 (pm20) cc_final: 0.7727 (pm20) REVERT: L 134 ASP cc_start: 0.8871 (m-30) cc_final: 0.8596 (m-30) REVERT: L 190 GLU cc_start: 0.9113 (tp30) cc_final: 0.8901 (tm-30) REVERT: L 191 ASP cc_start: 0.9316 (t70) cc_final: 0.9043 (t0) outliers start: 2 outliers final: 0 residues processed: 527 average time/residue: 0.1034 time to fit residues: 72.1516 Evaluate side-chains 428 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN E 145 GLN H 145 GLN I 145 GLN L 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.050525 restraints weight = 31319.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.052558 restraints weight = 17205.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.053988 restraints weight = 11070.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055017 restraints weight = 7779.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055742 restraints weight = 5773.056| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.121 Angle : 0.641 6.400 11472 Z= 0.307 Chirality : 0.040 0.139 1272 Planarity : 0.004 0.038 1452 Dihedral : 3.820 15.747 1092 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.34 % Allowed : 2.59 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.29), residues: 972 helix: 1.61 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.81 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 194 TYR 0.017 0.001 TYR L 146 PHE 0.017 0.002 PHE K 165 TRP 0.031 0.001 TRP J 131 HIS 0.004 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8448) covalent geometry : angle 0.64111 (11472) hydrogen bonds : bond 0.02362 ( 504) hydrogen bonds : angle 3.54011 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 531 time to evaluate : 0.350 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: A 145 GLN cc_start: 0.9525 (mt0) cc_final: 0.9299 (mt0) REVERT: A 158 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8769 (mtmm) REVERT: A 160 ARG cc_start: 0.9416 (mtt180) cc_final: 0.9188 (mtt180) REVERT: A 179 GLN cc_start: 0.9701 (tp40) cc_final: 0.9443 (tm-30) REVERT: A 190 GLU cc_start: 0.9237 (tp30) cc_final: 0.8929 (tp30) REVERT: A 193 GLU cc_start: 0.8766 (pp20) cc_final: 0.8489 (pp20) REVERT: B 114 PHE cc_start: 0.8711 (t80) cc_final: 0.8152 (t80) REVERT: B 117 GLN cc_start: 0.9547 (tm-30) cc_final: 0.9325 (tm-30) REVERT: B 128 ASN cc_start: 0.8962 (t0) cc_final: 0.8033 (t0) REVERT: B 145 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8887 (pm20) REVERT: B 176 LEU cc_start: 0.9759 (tt) cc_final: 0.9510 (tt) REVERT: B 190 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 191 ASP cc_start: 0.9093 (t0) cc_final: 0.8734 (t0) REVERT: C 114 PHE cc_start: 0.8860 (t80) cc_final: 0.8455 (t80) REVERT: C 130 GLU cc_start: 0.8753 (pm20) cc_final: 0.8193 (pm20) REVERT: C 131 TRP cc_start: 0.9412 (t-100) cc_final: 0.8959 (t60) REVERT: C 134 ASP cc_start: 0.8920 (m-30) cc_final: 0.8392 (m-30) REVERT: C 145 GLN cc_start: 0.9487 (mm-40) cc_final: 0.8931 (mm-40) REVERT: C 147 GLN cc_start: 0.9709 (mm-40) cc_final: 0.9399 (mm-40) REVERT: C 150 ARG cc_start: 0.9726 (mmm-85) cc_final: 0.9456 (mmm-85) REVERT: C 158 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8889 (mtmm) REVERT: C 165 PHE cc_start: 0.8989 (m-80) cc_final: 0.8646 (m-80) REVERT: C 173 CYS cc_start: 0.9489 (m) cc_final: 0.8940 (t) REVERT: C 174 LYS cc_start: 0.9516 (mtmm) cc_final: 0.9193 (mtmm) REVERT: C 190 GLU cc_start: 0.9279 (tp30) cc_final: 0.8910 (tm-30) REVERT: D 117 GLN cc_start: 0.9467 (tp-100) cc_final: 0.9184 (tp-100) REVERT: D 130 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 134 ASP cc_start: 0.8686 (m-30) cc_final: 0.8470 (m-30) REVERT: D 139 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8912 (mppt) REVERT: D 154 THR cc_start: 0.8068 (p) cc_final: 0.7826 (p) REVERT: D 158 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8511 (mttp) REVERT: D 165 PHE cc_start: 0.9526 (m-10) cc_final: 0.9254 (m-10) REVERT: D 169 TRP cc_start: 0.9264 (m-10) cc_final: 0.8828 (m-10) REVERT: D 179 GLN cc_start: 0.9533 (tm-30) cc_final: 0.9243 (tm-30) REVERT: D 184 SER cc_start: 0.9254 (t) cc_final: 0.9010 (t) REVERT: D 193 GLU cc_start: 0.8757 (pp20) cc_final: 0.8286 (pp20) REVERT: E 114 PHE cc_start: 0.8945 (t80) cc_final: 0.8708 (t80) REVERT: E 128 ASN cc_start: 0.8382 (t0) cc_final: 0.7565 (t0) REVERT: E 130 GLU cc_start: 0.8309 (pm20) cc_final: 0.7944 (pm20) REVERT: E 134 ASP cc_start: 0.9017 (m-30) cc_final: 0.8647 (m-30) REVERT: E 139 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9103 (mtmm) REVERT: E 143 ASP cc_start: 0.8613 (m-30) cc_final: 0.8390 (m-30) REVERT: E 147 GLN cc_start: 0.9591 (mm-40) cc_final: 0.9243 (mt0) REVERT: E 160 ARG cc_start: 0.9176 (mtm-85) cc_final: 0.8920 (mtm-85) REVERT: E 169 TRP cc_start: 0.9269 (m-10) cc_final: 0.8910 (m-10) REVERT: E 179 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9203 (tm-30) REVERT: E 190 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9108 (tp30) REVERT: F 130 GLU cc_start: 0.8880 (pm20) cc_final: 0.8659 (pm20) REVERT: F 134 ASP cc_start: 0.8775 (m-30) cc_final: 0.8233 (m-30) REVERT: F 143 ASP cc_start: 0.9536 (p0) cc_final: 0.9308 (p0) REVERT: F 145 GLN cc_start: 0.9418 (mt0) cc_final: 0.8908 (mt0) REVERT: F 165 PHE cc_start: 0.9340 (m-80) cc_final: 0.9028 (m-80) REVERT: G 143 ASP cc_start: 0.9198 (t70) cc_final: 0.7983 (t70) REVERT: G 144 GLU cc_start: 0.9045 (pm20) cc_final: 0.8839 (pm20) REVERT: G 147 GLN cc_start: 0.9649 (mm-40) cc_final: 0.8920 (mp10) REVERT: G 158 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8795 (mtmm) REVERT: G 160 ARG cc_start: 0.9557 (mtt180) cc_final: 0.9213 (mtt180) REVERT: G 175 ASP cc_start: 0.9604 (t70) cc_final: 0.9378 (t0) REVERT: G 190 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8698 (tm-30) REVERT: H 114 PHE cc_start: 0.8828 (t80) cc_final: 0.8610 (t80) REVERT: H 130 GLU cc_start: 0.8878 (pm20) cc_final: 0.8360 (pm20) REVERT: H 134 ASP cc_start: 0.8973 (m-30) cc_final: 0.8267 (m-30) REVERT: H 154 THR cc_start: 0.8752 (p) cc_final: 0.8475 (p) REVERT: H 158 LYS cc_start: 0.9253 (mttp) cc_final: 0.8947 (mttp) REVERT: H 179 GLN cc_start: 0.9580 (tm-30) cc_final: 0.9349 (tm-30) REVERT: H 190 GLU cc_start: 0.9021 (tp30) cc_final: 0.8691 (tp30) REVERT: I 128 ASN cc_start: 0.8983 (t0) cc_final: 0.8765 (t0) REVERT: I 134 ASP cc_start: 0.8457 (m-30) cc_final: 0.8108 (m-30) REVERT: I 143 ASP cc_start: 0.8549 (t70) cc_final: 0.7798 (t70) REVERT: I 147 GLN cc_start: 0.9585 (mm-40) cc_final: 0.9074 (mt0) REVERT: I 158 LYS cc_start: 0.9083 (mttp) cc_final: 0.8831 (mttp) REVERT: I 173 CYS cc_start: 0.9335 (m) cc_final: 0.8854 (t) REVERT: I 179 GLN cc_start: 0.9456 (tm-30) cc_final: 0.9143 (tm-30) REVERT: I 190 GLU cc_start: 0.9437 (mm-30) cc_final: 0.8905 (tp30) REVERT: I 193 GLU cc_start: 0.9252 (pp20) cc_final: 0.8715 (pp20) REVERT: J 114 PHE cc_start: 0.8816 (t80) cc_final: 0.8530 (t80) REVERT: J 128 ASN cc_start: 0.8613 (t0) cc_final: 0.8244 (t0) REVERT: J 130 GLU cc_start: 0.7534 (pp20) cc_final: 0.7194 (pp20) REVERT: J 134 ASP cc_start: 0.8922 (m-30) cc_final: 0.8165 (m-30) REVERT: J 143 ASP cc_start: 0.9146 (t70) cc_final: 0.8880 (t0) REVERT: J 145 GLN cc_start: 0.9541 (mt0) cc_final: 0.9303 (mt0) REVERT: J 158 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8537 (mttp) REVERT: J 160 ARG cc_start: 0.9497 (mtt180) cc_final: 0.9111 (mtt180) REVERT: J 174 LYS cc_start: 0.9418 (mttp) cc_final: 0.8958 (mtmm) REVERT: J 178 LEU cc_start: 0.9496 (tt) cc_final: 0.9165 (pp) REVERT: J 190 GLU cc_start: 0.9147 (tp30) cc_final: 0.8186 (tp30) REVERT: J 193 GLU cc_start: 0.8533 (pp20) cc_final: 0.7594 (pp20) REVERT: K 114 PHE cc_start: 0.8822 (t80) cc_final: 0.8561 (t80) REVERT: K 117 GLN cc_start: 0.9360 (tm-30) cc_final: 0.9126 (tm-30) REVERT: K 134 ASP cc_start: 0.8505 (m-30) cc_final: 0.8264 (m-30) REVERT: K 139 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9093 (mtmm) REVERT: K 179 GLN cc_start: 0.9392 (tm-30) cc_final: 0.9113 (tm-30) REVERT: K 190 GLU cc_start: 0.9007 (tp30) cc_final: 0.8364 (tp30) REVERT: K 193 GLU cc_start: 0.8537 (pp20) cc_final: 0.7948 (pp20) REVERT: L 116 ASP cc_start: 0.9261 (t70) cc_final: 0.9027 (t0) REVERT: L 130 GLU cc_start: 0.8193 (pm20) cc_final: 0.7870 (pm20) REVERT: L 134 ASP cc_start: 0.8886 (m-30) cc_final: 0.8615 (m-30) REVERT: L 174 LYS cc_start: 0.9628 (mttt) cc_final: 0.9198 (mttp) outliers start: 3 outliers final: 0 residues processed: 534 average time/residue: 0.1050 time to fit residues: 74.1214 Evaluate side-chains 445 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 145 GLN H 145 GLN I 145 GLN L 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.060589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.051677 restraints weight = 31030.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.053620 restraints weight = 17417.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.054971 restraints weight = 11286.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.055945 restraints weight = 7998.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.056665 restraints weight = 5988.101| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8448 Z= 0.121 Angle : 0.664 7.309 11472 Z= 0.317 Chirality : 0.040 0.154 1272 Planarity : 0.004 0.038 1452 Dihedral : 3.831 17.709 1092 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.23 % Allowed : 1.35 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.29), residues: 972 helix: 1.63 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.93 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 150 TYR 0.018 0.001 TYR L 146 PHE 0.017 0.002 PHE L 163 TRP 0.040 0.001 TRP I 131 HIS 0.004 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8448) covalent geometry : angle 0.66356 (11472) hydrogen bonds : bond 0.02374 ( 504) hydrogen bonds : angle 3.59325 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 542 time to evaluate : 0.400 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: A 158 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8759 (mtmm) REVERT: A 160 ARG cc_start: 0.9390 (mtt180) cc_final: 0.9187 (mtt180) REVERT: A 179 GLN cc_start: 0.9705 (tp40) cc_final: 0.9438 (tm-30) REVERT: A 190 GLU cc_start: 0.9208 (tp30) cc_final: 0.8912 (tp30) REVERT: A 193 GLU cc_start: 0.8714 (pp20) cc_final: 0.8485 (pp20) REVERT: B 112 LEU cc_start: 0.9056 (mp) cc_final: 0.8494 (mp) REVERT: B 114 PHE cc_start: 0.8468 (t80) cc_final: 0.8224 (t80) REVERT: B 117 GLN cc_start: 0.9555 (tm-30) cc_final: 0.9329 (tm-30) REVERT: B 126 VAL cc_start: 0.9362 (t) cc_final: 0.9159 (p) REVERT: B 128 ASN cc_start: 0.8894 (t0) cc_final: 0.7993 (t0) REVERT: B 175 ASP cc_start: 0.9561 (t0) cc_final: 0.9267 (m-30) REVERT: B 179 GLN cc_start: 0.9572 (tm-30) cc_final: 0.9370 (tm-30) REVERT: B 190 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8841 (tm-30) REVERT: B 191 ASP cc_start: 0.9080 (t0) cc_final: 0.8716 (t0) REVERT: C 114 PHE cc_start: 0.8891 (t80) cc_final: 0.8220 (t80) REVERT: C 130 GLU cc_start: 0.8786 (pm20) cc_final: 0.8217 (pm20) REVERT: C 131 TRP cc_start: 0.9426 (t-100) cc_final: 0.8961 (t60) REVERT: C 134 ASP cc_start: 0.8931 (m-30) cc_final: 0.8422 (m-30) REVERT: C 143 ASP cc_start: 0.9152 (t70) cc_final: 0.8923 (t70) REVERT: C 145 GLN cc_start: 0.9458 (mm-40) cc_final: 0.8996 (mm-40) REVERT: C 147 GLN cc_start: 0.9731 (mm-40) cc_final: 0.9390 (mm-40) REVERT: C 150 ARG cc_start: 0.9729 (mmm-85) cc_final: 0.9445 (mmm-85) REVERT: C 158 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8883 (mtmm) REVERT: C 165 PHE cc_start: 0.9040 (m-80) cc_final: 0.8694 (m-80) REVERT: C 173 CYS cc_start: 0.9488 (m) cc_final: 0.8958 (t) REVERT: C 174 LYS cc_start: 0.9537 (mtmm) cc_final: 0.9208 (mtmm) REVERT: C 187 TYR cc_start: 0.8922 (p90) cc_final: 0.8719 (p90) REVERT: C 191 ASP cc_start: 0.9219 (t70) cc_final: 0.8824 (t0) REVERT: D 117 GLN cc_start: 0.9452 (tp-100) cc_final: 0.9172 (tp-100) REVERT: D 130 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7248 (tm-30) REVERT: D 134 ASP cc_start: 0.8610 (m-30) cc_final: 0.8343 (m-30) REVERT: D 139 LYS cc_start: 0.9287 (mtmm) cc_final: 0.8963 (mppt) REVERT: D 154 THR cc_start: 0.8068 (p) cc_final: 0.7818 (p) REVERT: D 158 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8491 (mttp) REVERT: D 169 TRP cc_start: 0.9245 (m-10) cc_final: 0.8810 (m-10) REVERT: D 179 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9248 (tm-30) REVERT: D 184 SER cc_start: 0.9203 (t) cc_final: 0.8930 (t) REVERT: D 193 GLU cc_start: 0.8785 (pp20) cc_final: 0.8264 (pp20) REVERT: E 114 PHE cc_start: 0.8915 (t80) cc_final: 0.8416 (t80) REVERT: E 128 ASN cc_start: 0.8373 (t0) cc_final: 0.7378 (t0) REVERT: E 130 GLU cc_start: 0.8376 (pm20) cc_final: 0.8048 (pm20) REVERT: E 134 ASP cc_start: 0.9011 (m-30) cc_final: 0.8723 (m-30) REVERT: E 139 LYS cc_start: 0.9404 (mtmm) cc_final: 0.9117 (mtmm) REVERT: E 143 ASP cc_start: 0.8588 (m-30) cc_final: 0.8366 (m-30) REVERT: E 144 GLU cc_start: 0.8313 (tt0) cc_final: 0.7772 (tt0) REVERT: E 147 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9254 (mt0) REVERT: E 155 ASN cc_start: 0.8488 (m110) cc_final: 0.8103 (m-40) REVERT: E 158 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8743 (mttp) REVERT: E 160 ARG cc_start: 0.9158 (mtm-85) cc_final: 0.8880 (mtm-85) REVERT: E 169 TRP cc_start: 0.9315 (m-10) cc_final: 0.8907 (m-10) REVERT: E 179 GLN cc_start: 0.9455 (tm-30) cc_final: 0.9249 (tm-30) REVERT: E 190 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9086 (tp30) REVERT: F 130 GLU cc_start: 0.8898 (pm20) cc_final: 0.8683 (pm20) REVERT: F 134 ASP cc_start: 0.8797 (m-30) cc_final: 0.8224 (m-30) REVERT: F 143 ASP cc_start: 0.9540 (p0) cc_final: 0.9291 (p0) REVERT: F 145 GLN cc_start: 0.9384 (mt0) cc_final: 0.8784 (mt0) REVERT: F 164 SER cc_start: 0.9588 (p) cc_final: 0.9382 (p) REVERT: F 165 PHE cc_start: 0.9347 (m-80) cc_final: 0.8996 (m-80) REVERT: F 190 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8774 (tm-30) REVERT: F 191 ASP cc_start: 0.9277 (t70) cc_final: 0.9073 (t0) REVERT: G 117 GLN cc_start: 0.9479 (tm-30) cc_final: 0.9237 (tm-30) REVERT: G 130 GLU cc_start: 0.8212 (pm20) cc_final: 0.7681 (pm20) REVERT: G 158 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8778 (mtmm) REVERT: G 160 ARG cc_start: 0.9568 (mtt180) cc_final: 0.9275 (mtt180) REVERT: G 175 ASP cc_start: 0.9611 (t70) cc_final: 0.9408 (t0) REVERT: G 190 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8283 (tm-30) REVERT: H 114 PHE cc_start: 0.8866 (t80) cc_final: 0.8517 (t80) REVERT: H 117 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9234 (tm-30) REVERT: H 130 GLU cc_start: 0.8946 (pm20) cc_final: 0.8526 (pm20) REVERT: H 134 ASP cc_start: 0.8992 (m-30) cc_final: 0.8377 (m-30) REVERT: H 154 THR cc_start: 0.8691 (p) cc_final: 0.8392 (p) REVERT: H 158 LYS cc_start: 0.9246 (mttp) cc_final: 0.8959 (mttp) REVERT: H 179 GLN cc_start: 0.9565 (tm-30) cc_final: 0.9330 (tm-30) REVERT: H 190 GLU cc_start: 0.8982 (tp30) cc_final: 0.8663 (tp30) REVERT: I 128 ASN cc_start: 0.8866 (t0) cc_final: 0.8632 (t0) REVERT: I 130 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7039 (tm-30) REVERT: I 134 ASP cc_start: 0.8536 (m-30) cc_final: 0.8147 (m-30) REVERT: I 143 ASP cc_start: 0.8586 (t70) cc_final: 0.7791 (t70) REVERT: I 147 GLN cc_start: 0.9585 (mm-40) cc_final: 0.9064 (mt0) REVERT: I 158 LYS cc_start: 0.8980 (mttp) cc_final: 0.8670 (mttp) REVERT: I 173 CYS cc_start: 0.9363 (m) cc_final: 0.8806 (t) REVERT: I 179 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9157 (tm-30) REVERT: I 190 GLU cc_start: 0.9490 (mm-30) cc_final: 0.8994 (tp30) REVERT: I 193 GLU cc_start: 0.9147 (pp20) cc_final: 0.8929 (pp20) REVERT: J 114 PHE cc_start: 0.8795 (t80) cc_final: 0.8591 (t80) REVERT: J 128 ASN cc_start: 0.8668 (t0) cc_final: 0.8361 (t0) REVERT: J 130 GLU cc_start: 0.7337 (pp20) cc_final: 0.6996 (pp20) REVERT: J 134 ASP cc_start: 0.8908 (m-30) cc_final: 0.8177 (m-30) REVERT: J 143 ASP cc_start: 0.9157 (t70) cc_final: 0.8878 (t0) REVERT: J 145 GLN cc_start: 0.9536 (mt0) cc_final: 0.9305 (mt0) REVERT: J 154 THR cc_start: 0.8162 (p) cc_final: 0.7848 (p) REVERT: J 158 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8552 (mtmm) REVERT: J 165 PHE cc_start: 0.9486 (m-10) cc_final: 0.9125 (m-10) REVERT: J 173 CYS cc_start: 0.9401 (m) cc_final: 0.8869 (t) REVERT: J 174 LYS cc_start: 0.9433 (mttp) cc_final: 0.9148 (mtmm) REVERT: J 190 GLU cc_start: 0.9152 (tp30) cc_final: 0.8576 (tp30) REVERT: K 114 PHE cc_start: 0.8811 (t80) cc_final: 0.8492 (t80) REVERT: K 117 GLN cc_start: 0.9369 (tm-30) cc_final: 0.9149 (tm-30) REVERT: K 134 ASP cc_start: 0.8598 (m-30) cc_final: 0.8249 (m-30) REVERT: K 139 LYS cc_start: 0.9393 (mtmm) cc_final: 0.9090 (mtmm) REVERT: K 179 GLN cc_start: 0.9431 (tm-30) cc_final: 0.9152 (tm-30) REVERT: K 190 GLU cc_start: 0.9013 (tp30) cc_final: 0.8312 (tp30) REVERT: K 193 GLU cc_start: 0.8519 (pp20) cc_final: 0.7861 (pp20) REVERT: L 116 ASP cc_start: 0.9258 (t70) cc_final: 0.9029 (t0) REVERT: L 126 VAL cc_start: 0.9409 (t) cc_final: 0.9141 (p) REVERT: L 134 ASP cc_start: 0.8882 (m-30) cc_final: 0.8639 (m-30) REVERT: L 143 ASP cc_start: 0.8915 (t70) cc_final: 0.8686 (t0) REVERT: L 174 LYS cc_start: 0.9619 (mttt) cc_final: 0.9230 (mttp) outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.1053 time to fit residues: 75.7466 Evaluate side-chains 449 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 145 GLN H 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.058253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.049647 restraints weight = 31781.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.051553 restraints weight = 17546.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.052889 restraints weight = 11268.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.053854 restraints weight = 7884.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.054566 restraints weight = 5845.704| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8448 Z= 0.184 Angle : 0.696 6.805 11472 Z= 0.341 Chirality : 0.042 0.147 1272 Planarity : 0.005 0.039 1452 Dihedral : 4.165 19.125 1092 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.11 % Allowed : 1.01 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.29), residues: 972 helix: 1.54 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -2.09 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 194 TYR 0.018 0.001 TYR L 146 PHE 0.021 0.002 PHE F 163 TRP 0.024 0.001 TRP L 131 HIS 0.005 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8448) covalent geometry : angle 0.69624 (11472) hydrogen bonds : bond 0.02973 ( 504) hydrogen bonds : angle 4.03211 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 0.369 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: A 129 VAL cc_start: 0.9603 (p) cc_final: 0.9359 (p) REVERT: A 145 GLN cc_start: 0.9503 (mt0) cc_final: 0.9277 (mt0) REVERT: A 154 THR cc_start: 0.8359 (p) cc_final: 0.8146 (p) REVERT: A 158 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8731 (mtmm) REVERT: A 179 GLN cc_start: 0.9683 (tp40) cc_final: 0.9430 (tm-30) REVERT: A 190 GLU cc_start: 0.9195 (tp30) cc_final: 0.8917 (tp30) REVERT: A 193 GLU cc_start: 0.8883 (pp20) cc_final: 0.8639 (pp20) REVERT: B 114 PHE cc_start: 0.8596 (t80) cc_final: 0.8288 (t80) REVERT: B 117 GLN cc_start: 0.9533 (tm-30) cc_final: 0.9258 (tm-30) REVERT: B 128 ASN cc_start: 0.8805 (t0) cc_final: 0.8201 (t0) REVERT: B 129 VAL cc_start: 0.9807 (p) cc_final: 0.9562 (p) REVERT: B 190 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8849 (tm-30) REVERT: B 191 ASP cc_start: 0.9095 (t0) cc_final: 0.8772 (t0) REVERT: C 114 PHE cc_start: 0.8819 (t80) cc_final: 0.8414 (t80) REVERT: C 117 GLN cc_start: 0.9504 (tm-30) cc_final: 0.9284 (tm-30) REVERT: C 134 ASP cc_start: 0.8931 (m-30) cc_final: 0.8375 (m-30) REVERT: C 143 ASP cc_start: 0.9136 (t70) cc_final: 0.8818 (t0) REVERT: C 147 GLN cc_start: 0.9726 (mm-40) cc_final: 0.9358 (mm-40) REVERT: C 158 LYS cc_start: 0.9343 (mtmm) cc_final: 0.9025 (mtmm) REVERT: C 174 LYS cc_start: 0.9600 (mtmm) cc_final: 0.9260 (mtmm) REVERT: D 117 GLN cc_start: 0.9472 (tp-100) cc_final: 0.9153 (tp-100) REVERT: D 134 ASP cc_start: 0.8560 (m-30) cc_final: 0.8246 (m-30) REVERT: D 154 THR cc_start: 0.8275 (p) cc_final: 0.7998 (p) REVERT: D 158 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8581 (mttp) REVERT: D 169 TRP cc_start: 0.9422 (m-10) cc_final: 0.9114 (m-10) REVERT: D 179 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9243 (tm-30) REVERT: E 114 PHE cc_start: 0.8866 (t80) cc_final: 0.8626 (t80) REVERT: E 128 ASN cc_start: 0.8552 (t0) cc_final: 0.7461 (t0) REVERT: E 130 GLU cc_start: 0.8436 (pm20) cc_final: 0.8020 (pm20) REVERT: E 134 ASP cc_start: 0.9029 (m-30) cc_final: 0.8771 (m-30) REVERT: E 139 LYS cc_start: 0.9408 (mtmm) cc_final: 0.9124 (mtmm) REVERT: E 144 GLU cc_start: 0.8385 (tt0) cc_final: 0.7876 (tt0) REVERT: E 147 GLN cc_start: 0.9620 (mm-40) cc_final: 0.9290 (mt0) REVERT: E 155 ASN cc_start: 0.8765 (m110) cc_final: 0.8298 (m-40) REVERT: E 158 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8713 (mtmm) REVERT: E 160 ARG cc_start: 0.9153 (mtm-85) cc_final: 0.8882 (mtm-85) REVERT: E 169 TRP cc_start: 0.9364 (m-10) cc_final: 0.9052 (m-10) REVERT: E 190 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9062 (tp30) REVERT: F 134 ASP cc_start: 0.8808 (m-30) cc_final: 0.8395 (m-30) REVERT: F 145 GLN cc_start: 0.9397 (mt0) cc_final: 0.8739 (mt0) REVERT: F 165 PHE cc_start: 0.9476 (m-80) cc_final: 0.9128 (m-80) REVERT: F 173 CYS cc_start: 0.9454 (m) cc_final: 0.9013 (t) REVERT: F 191 ASP cc_start: 0.9273 (t70) cc_final: 0.9041 (t0) REVERT: G 117 GLN cc_start: 0.9481 (tm-30) cc_final: 0.9184 (tm-30) REVERT: G 130 GLU cc_start: 0.8356 (pm20) cc_final: 0.7824 (pm20) REVERT: G 158 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8825 (mtmm) REVERT: G 190 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8724 (tm-30) REVERT: H 130 GLU cc_start: 0.9019 (pm20) cc_final: 0.8641 (pm20) REVERT: H 134 ASP cc_start: 0.8912 (m-30) cc_final: 0.8564 (m-30) REVERT: H 154 THR cc_start: 0.8868 (p) cc_final: 0.8642 (p) REVERT: H 158 LYS cc_start: 0.9232 (mttp) cc_final: 0.8969 (mttm) REVERT: H 179 GLN cc_start: 0.9562 (tm-30) cc_final: 0.9333 (tm-30) REVERT: I 128 ASN cc_start: 0.8968 (t0) cc_final: 0.8744 (t0) REVERT: I 134 ASP cc_start: 0.8467 (m-30) cc_final: 0.8107 (m-30) REVERT: I 143 ASP cc_start: 0.8644 (t70) cc_final: 0.8269 (t70) REVERT: I 147 GLN cc_start: 0.9608 (mm-40) cc_final: 0.9230 (mt0) REVERT: I 158 LYS cc_start: 0.9153 (mttp) cc_final: 0.8861 (mttp) REVERT: I 159 MET cc_start: 0.9350 (tpp) cc_final: 0.8955 (mmm) REVERT: I 173 CYS cc_start: 0.9393 (m) cc_final: 0.8830 (t) REVERT: I 179 GLN cc_start: 0.9448 (tm-30) cc_final: 0.9171 (tm-30) REVERT: I 190 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8318 (tp30) REVERT: I 193 GLU cc_start: 0.9084 (pp20) cc_final: 0.8063 (pp20) REVERT: J 128 ASN cc_start: 0.8689 (t0) cc_final: 0.8423 (t0) REVERT: J 129 VAL cc_start: 0.9515 (p) cc_final: 0.9276 (p) REVERT: J 130 GLU cc_start: 0.7349 (pp20) cc_final: 0.6661 (pp20) REVERT: J 134 ASP cc_start: 0.8903 (m-30) cc_final: 0.7888 (m-30) REVERT: J 143 ASP cc_start: 0.9065 (t70) cc_final: 0.8815 (t0) REVERT: J 173 CYS cc_start: 0.9383 (m) cc_final: 0.8832 (t) REVERT: J 174 LYS cc_start: 0.9474 (mttp) cc_final: 0.9229 (mtmm) REVERT: J 193 GLU cc_start: 0.8315 (pp20) cc_final: 0.8052 (pp20) REVERT: K 114 PHE cc_start: 0.8839 (t80) cc_final: 0.8445 (t80) REVERT: K 117 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9082 (tm-30) REVERT: K 134 ASP cc_start: 0.8610 (m-30) cc_final: 0.8323 (m-30) REVERT: K 139 LYS cc_start: 0.9418 (mtmm) cc_final: 0.9140 (mtmm) REVERT: K 160 ARG cc_start: 0.9212 (mtt180) cc_final: 0.8362 (mtt180) REVERT: K 179 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9154 (tm-30) REVERT: K 190 GLU cc_start: 0.8932 (tp30) cc_final: 0.8102 (tp30) REVERT: K 193 GLU cc_start: 0.8591 (pp20) cc_final: 0.8004 (pp20) REVERT: L 116 ASP cc_start: 0.9143 (t70) cc_final: 0.8909 (t0) REVERT: L 130 GLU cc_start: 0.8641 (pm20) cc_final: 0.8160 (pm20) REVERT: L 131 TRP cc_start: 0.8781 (t60) cc_final: 0.8470 (t60) REVERT: L 134 ASP cc_start: 0.8925 (m-30) cc_final: 0.8322 (m-30) REVERT: L 174 LYS cc_start: 0.9640 (mttt) cc_final: 0.9250 (mttp) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.1081 time to fit residues: 71.9129 Evaluate side-chains 434 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.058010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.049346 restraints weight = 31805.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.051260 restraints weight = 17422.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.052583 restraints weight = 11144.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.053501 restraints weight = 7846.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.054223 restraints weight = 5872.273| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8448 Z= 0.188 Angle : 0.728 7.513 11472 Z= 0.357 Chirality : 0.042 0.185 1272 Planarity : 0.005 0.051 1452 Dihedral : 4.392 21.725 1092 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 972 helix: 1.52 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -2.25 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 194 TYR 0.019 0.001 TYR L 146 PHE 0.021 0.002 PHE K 165 TRP 0.014 0.001 TRP J 131 HIS 0.004 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8448) covalent geometry : angle 0.72757 (11472) hydrogen bonds : bond 0.03073 ( 504) hydrogen bonds : angle 4.17143 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 0.353 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: A 125 ARG cc_start: 0.9392 (tpp80) cc_final: 0.8952 (tpp80) REVERT: A 134 ASP cc_start: 0.9005 (m-30) cc_final: 0.8464 (m-30) REVERT: A 145 GLN cc_start: 0.9509 (mt0) cc_final: 0.9259 (mt0) REVERT: A 154 THR cc_start: 0.8399 (p) cc_final: 0.8193 (p) REVERT: A 158 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8749 (mtmm) REVERT: A 179 GLN cc_start: 0.9684 (tp40) cc_final: 0.9443 (tm-30) REVERT: A 190 GLU cc_start: 0.9179 (tp30) cc_final: 0.8916 (tp30) REVERT: A 193 GLU cc_start: 0.8920 (pp20) cc_final: 0.8687 (pp20) REVERT: B 114 PHE cc_start: 0.8607 (t80) cc_final: 0.8265 (t80) REVERT: B 117 GLN cc_start: 0.9533 (tm-30) cc_final: 0.9255 (tm-30) REVERT: B 125 ARG cc_start: 0.9190 (mmm-85) cc_final: 0.8814 (mmm-85) REVERT: B 128 ASN cc_start: 0.8981 (t0) cc_final: 0.8209 (t0) REVERT: B 129 VAL cc_start: 0.9756 (p) cc_final: 0.9507 (p) REVERT: B 144 GLU cc_start: 0.9095 (pm20) cc_final: 0.8811 (pm20) REVERT: B 147 GLN cc_start: 0.9255 (mt0) cc_final: 0.8770 (mp10) REVERT: B 179 GLN cc_start: 0.9595 (tm-30) cc_final: 0.9389 (tm-30) REVERT: B 190 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8876 (tm-30) REVERT: B 191 ASP cc_start: 0.9127 (t0) cc_final: 0.8800 (t0) REVERT: C 114 PHE cc_start: 0.8794 (t80) cc_final: 0.8326 (t80) REVERT: C 117 GLN cc_start: 0.9504 (tm-30) cc_final: 0.9231 (tm-30) REVERT: C 134 ASP cc_start: 0.8881 (m-30) cc_final: 0.8617 (m-30) REVERT: C 143 ASP cc_start: 0.9190 (t70) cc_final: 0.8950 (t0) REVERT: C 147 GLN cc_start: 0.9737 (mm-40) cc_final: 0.9367 (mm-40) REVERT: C 150 ARG cc_start: 0.9654 (mmm-85) cc_final: 0.9406 (mmm-85) REVERT: C 158 LYS cc_start: 0.9398 (mtmm) cc_final: 0.9027 (mtmm) REVERT: C 174 LYS cc_start: 0.9591 (mtmm) cc_final: 0.9259 (mtmm) REVERT: C 190 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8797 (tm-30) REVERT: C 191 ASP cc_start: 0.9219 (t70) cc_final: 0.8962 (t0) REVERT: D 117 GLN cc_start: 0.9458 (tp-100) cc_final: 0.9142 (tp-100) REVERT: D 134 ASP cc_start: 0.8540 (m-30) cc_final: 0.8208 (m-30) REVERT: D 139 LYS cc_start: 0.9328 (mtmm) cc_final: 0.8960 (mtmm) REVERT: D 147 GLN cc_start: 0.9255 (mt0) cc_final: 0.9016 (mt0) REVERT: D 158 LYS cc_start: 0.9008 (mtmm) cc_final: 0.8594 (mtmm) REVERT: D 169 TRP cc_start: 0.9437 (m-10) cc_final: 0.9150 (m-10) REVERT: D 179 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9253 (tm-30) REVERT: E 114 PHE cc_start: 0.8870 (t80) cc_final: 0.8646 (t80) REVERT: E 128 ASN cc_start: 0.8610 (t0) cc_final: 0.8368 (t0) REVERT: E 134 ASP cc_start: 0.9006 (m-30) cc_final: 0.8776 (m-30) REVERT: E 139 LYS cc_start: 0.9420 (mtmm) cc_final: 0.9118 (mtmm) REVERT: E 147 GLN cc_start: 0.9614 (mm-40) cc_final: 0.9261 (mt0) REVERT: E 155 ASN cc_start: 0.8818 (m110) cc_final: 0.8390 (m-40) REVERT: E 158 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8723 (mtmm) REVERT: E 160 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8774 (mtm-85) REVERT: E 169 TRP cc_start: 0.9383 (m-10) cc_final: 0.9106 (m-10) REVERT: E 190 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9058 (tp30) REVERT: F 128 ASN cc_start: 0.8910 (t0) cc_final: 0.7688 (t0) REVERT: F 129 VAL cc_start: 0.9796 (m) cc_final: 0.9524 (p) REVERT: F 130 GLU cc_start: 0.8784 (pm20) cc_final: 0.8568 (pm20) REVERT: F 134 ASP cc_start: 0.8784 (m-30) cc_final: 0.8422 (m-30) REVERT: F 143 ASP cc_start: 0.9539 (p0) cc_final: 0.9338 (p0) REVERT: F 145 GLN cc_start: 0.9410 (mt0) cc_final: 0.8805 (mt0) REVERT: F 158 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8793 (mtmm) REVERT: F 165 PHE cc_start: 0.9521 (m-80) cc_final: 0.9136 (m-80) REVERT: F 173 CYS cc_start: 0.9414 (m) cc_final: 0.9018 (t) REVERT: F 174 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9134 (mtmm) REVERT: F 190 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8756 (tm-30) REVERT: F 191 ASP cc_start: 0.9281 (t70) cc_final: 0.9075 (t0) REVERT: G 114 PHE cc_start: 0.8675 (t80) cc_final: 0.8469 (t80) REVERT: G 117 GLN cc_start: 0.9449 (tm-30) cc_final: 0.9058 (tm-30) REVERT: G 158 LYS cc_start: 0.9261 (mtmm) cc_final: 0.8897 (mtmm) REVERT: G 160 ARG cc_start: 0.9636 (mtm-85) cc_final: 0.9420 (mtm-85) REVERT: G 190 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8751 (tm-30) REVERT: H 117 GLN cc_start: 0.9498 (tm-30) cc_final: 0.9190 (tm-30) REVERT: H 130 GLU cc_start: 0.9051 (pm20) cc_final: 0.8613 (pm20) REVERT: H 134 ASP cc_start: 0.8895 (m-30) cc_final: 0.8551 (m-30) REVERT: H 158 LYS cc_start: 0.9243 (mttp) cc_final: 0.9004 (mttm) REVERT: H 179 GLN cc_start: 0.9567 (tm-30) cc_final: 0.9333 (tm-30) REVERT: H 190 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8849 (tm-30) REVERT: H 193 GLU cc_start: 0.8982 (pm20) cc_final: 0.8703 (pm20) REVERT: I 134 ASP cc_start: 0.8471 (m-30) cc_final: 0.8116 (m-30) REVERT: I 143 ASP cc_start: 0.8589 (t70) cc_final: 0.8173 (t70) REVERT: I 147 GLN cc_start: 0.9606 (mm-40) cc_final: 0.9194 (mt0) REVERT: I 173 CYS cc_start: 0.9423 (m) cc_final: 0.8804 (t) REVERT: I 179 GLN cc_start: 0.9475 (tm-30) cc_final: 0.9200 (tm-30) REVERT: I 190 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8330 (tp30) REVERT: I 193 GLU cc_start: 0.9088 (pp20) cc_final: 0.8111 (pp20) REVERT: J 128 ASN cc_start: 0.8679 (t0) cc_final: 0.8432 (t0) REVERT: J 130 GLU cc_start: 0.7389 (pp20) cc_final: 0.6716 (pp20) REVERT: J 134 ASP cc_start: 0.8888 (m-30) cc_final: 0.7757 (m-30) REVERT: J 143 ASP cc_start: 0.9038 (t70) cc_final: 0.8798 (t0) REVERT: J 174 LYS cc_start: 0.9465 (mttp) cc_final: 0.9203 (mtmm) REVERT: J 179 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9291 (tm-30) REVERT: J 193 GLU cc_start: 0.8798 (pp20) cc_final: 0.8043 (pp20) REVERT: K 112 LEU cc_start: 0.9114 (mt) cc_final: 0.8656 (mm) REVERT: K 114 PHE cc_start: 0.8719 (t80) cc_final: 0.8408 (t80) REVERT: K 117 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9059 (tm-30) REVERT: K 139 LYS cc_start: 0.9418 (mtmm) cc_final: 0.9107 (mtmm) REVERT: K 173 CYS cc_start: 0.9431 (m) cc_final: 0.9158 (t) REVERT: K 179 GLN cc_start: 0.9436 (tm-30) cc_final: 0.9144 (tm-30) REVERT: K 190 GLU cc_start: 0.8896 (tp30) cc_final: 0.8091 (tp30) REVERT: K 193 GLU cc_start: 0.8603 (pp20) cc_final: 0.8052 (pp20) REVERT: L 134 ASP cc_start: 0.8925 (m-30) cc_final: 0.8673 (m-30) REVERT: L 174 LYS cc_start: 0.9643 (mttt) cc_final: 0.9261 (mttp) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.1098 time to fit residues: 70.8428 Evaluate side-chains 414 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 0.9990 chunk 95 optimal weight: 0.0060 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 145 GLN H 145 GLN I 145 GLN I 155 ASN L 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.061223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.052164 restraints weight = 31120.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.054232 restraints weight = 16928.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.055694 restraints weight = 10781.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.056713 restraints weight = 7484.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.057469 restraints weight = 5499.568| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8448 Z= 0.131 Angle : 0.736 8.564 11472 Z= 0.352 Chirality : 0.042 0.172 1272 Planarity : 0.005 0.057 1452 Dihedral : 4.345 20.113 1092 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.23 % Allowed : 0.68 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 972 helix: 1.53 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -2.35 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 194 TYR 0.019 0.001 TYR L 146 PHE 0.026 0.002 PHE K 163 TRP 0.029 0.001 TRP J 131 HIS 0.006 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8448) covalent geometry : angle 0.73587 (11472) hydrogen bonds : bond 0.02480 ( 504) hydrogen bonds : angle 3.87847 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 528 time to evaluate : 0.366 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: A 114 PHE cc_start: 0.8844 (t80) cc_final: 0.8594 (t80) REVERT: A 117 GLN cc_start: 0.9418 (tm-30) cc_final: 0.9190 (tm-30) REVERT: A 125 ARG cc_start: 0.9337 (tpp80) cc_final: 0.8934 (tpp80) REVERT: A 134 ASP cc_start: 0.8966 (m-30) cc_final: 0.8313 (m-30) REVERT: A 143 ASP cc_start: 0.9133 (t0) cc_final: 0.8111 (t70) REVERT: A 145 GLN cc_start: 0.9557 (mt0) cc_final: 0.9269 (mt0) REVERT: A 147 GLN cc_start: 0.9598 (mm-40) cc_final: 0.8897 (mp10) REVERT: A 158 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8790 (mtmm) REVERT: A 174 LYS cc_start: 0.9583 (mttt) cc_final: 0.9195 (mttp) REVERT: A 179 GLN cc_start: 0.9689 (tp40) cc_final: 0.9480 (tm-30) REVERT: A 190 GLU cc_start: 0.9203 (tp30) cc_final: 0.8912 (tp30) REVERT: B 114 PHE cc_start: 0.8383 (t80) cc_final: 0.8104 (t80) REVERT: B 117 GLN cc_start: 0.9560 (tm-30) cc_final: 0.9304 (tm-30) REVERT: B 125 ARG cc_start: 0.9063 (mmm-85) cc_final: 0.8638 (mmm-85) REVERT: B 128 ASN cc_start: 0.8950 (t0) cc_final: 0.8144 (t0) REVERT: B 129 VAL cc_start: 0.9722 (p) cc_final: 0.9446 (p) REVERT: B 130 GLU cc_start: 0.8818 (pm20) cc_final: 0.8610 (pm20) REVERT: B 144 GLU cc_start: 0.9096 (pm20) cc_final: 0.8792 (pm20) REVERT: B 147 GLN cc_start: 0.9202 (mt0) cc_final: 0.8731 (mp10) REVERT: B 175 ASP cc_start: 0.9519 (t70) cc_final: 0.9236 (m-30) REVERT: B 179 GLN cc_start: 0.9619 (tm-30) cc_final: 0.9406 (tm-30) REVERT: B 190 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8869 (tm-30) REVERT: B 191 ASP cc_start: 0.9142 (t0) cc_final: 0.8836 (t0) REVERT: C 114 PHE cc_start: 0.8560 (t80) cc_final: 0.8337 (t80) REVERT: C 134 ASP cc_start: 0.8881 (m-30) cc_final: 0.8574 (m-30) REVERT: C 143 ASP cc_start: 0.9242 (t70) cc_final: 0.8968 (t70) REVERT: C 147 GLN cc_start: 0.9751 (mm-40) cc_final: 0.9404 (mm-40) REVERT: C 158 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8896 (mtmm) REVERT: C 169 TRP cc_start: 0.9103 (m-10) cc_final: 0.8859 (m-10) REVERT: C 173 CYS cc_start: 0.9536 (m) cc_final: 0.8964 (t) REVERT: C 190 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 191 ASP cc_start: 0.9283 (t70) cc_final: 0.9014 (t0) REVERT: D 117 GLN cc_start: 0.9443 (tp-100) cc_final: 0.9167 (tp-100) REVERT: D 134 ASP cc_start: 0.8524 (m-30) cc_final: 0.8190 (m-30) REVERT: D 139 LYS cc_start: 0.9363 (mtmm) cc_final: 0.8996 (mtmm) REVERT: D 147 GLN cc_start: 0.9330 (mt0) cc_final: 0.8811 (mt0) REVERT: D 158 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8462 (mttp) REVERT: D 169 TRP cc_start: 0.9349 (m-10) cc_final: 0.9060 (m-10) REVERT: D 179 GLN cc_start: 0.9526 (tm-30) cc_final: 0.9267 (tm-30) REVERT: D 193 GLU cc_start: 0.8789 (pm20) cc_final: 0.8103 (pm20) REVERT: E 114 PHE cc_start: 0.8582 (t80) cc_final: 0.8302 (t80) REVERT: E 134 ASP cc_start: 0.9054 (m-30) cc_final: 0.8757 (m-30) REVERT: E 139 LYS cc_start: 0.9456 (mtmm) cc_final: 0.9154 (mtmm) REVERT: E 143 ASP cc_start: 0.8707 (m-30) cc_final: 0.8465 (m-30) REVERT: E 144 GLU cc_start: 0.8453 (tt0) cc_final: 0.8245 (tt0) REVERT: E 147 GLN cc_start: 0.9624 (mm-40) cc_final: 0.9258 (mt0) REVERT: E 155 ASN cc_start: 0.8462 (m110) cc_final: 0.8167 (m-40) REVERT: E 158 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8653 (mtmm) REVERT: E 169 TRP cc_start: 0.9293 (m-10) cc_final: 0.8994 (m-10) REVERT: E 190 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9055 (tp30) REVERT: F 130 GLU cc_start: 0.8666 (pm20) cc_final: 0.8443 (pm20) REVERT: F 134 ASP cc_start: 0.8818 (m-30) cc_final: 0.8417 (m-30) REVERT: F 145 GLN cc_start: 0.9388 (mt0) cc_final: 0.8830 (mt0) REVERT: F 158 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8712 (mtmm) REVERT: F 165 PHE cc_start: 0.9498 (m-80) cc_final: 0.9202 (m-80) REVERT: F 173 CYS cc_start: 0.9480 (m) cc_final: 0.9024 (t) REVERT: F 174 LYS cc_start: 0.9420 (mtmm) cc_final: 0.9085 (mtmm) REVERT: F 175 ASP cc_start: 0.9554 (t70) cc_final: 0.9248 (m-30) REVERT: F 179 GLN cc_start: 0.9610 (tm-30) cc_final: 0.9376 (tm-30) REVERT: F 191 ASP cc_start: 0.9327 (t70) cc_final: 0.9100 (t0) REVERT: G 117 GLN cc_start: 0.9465 (tm-30) cc_final: 0.9163 (tm-30) REVERT: G 129 VAL cc_start: 0.9469 (p) cc_final: 0.9138 (p) REVERT: G 130 GLU cc_start: 0.8406 (pm20) cc_final: 0.8030 (pm20) REVERT: G 158 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8853 (mtmm) REVERT: G 173 CYS cc_start: 0.9361 (m) cc_final: 0.8768 (t) REVERT: G 190 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8726 (tm-30) REVERT: H 114 PHE cc_start: 0.8847 (t80) cc_final: 0.8527 (t80) REVERT: H 117 GLN cc_start: 0.9492 (tm-30) cc_final: 0.9192 (tm-30) REVERT: H 134 ASP cc_start: 0.8934 (m-30) cc_final: 0.8632 (m-30) REVERT: H 158 LYS cc_start: 0.9185 (mttp) cc_final: 0.8952 (mttp) REVERT: H 173 CYS cc_start: 0.9573 (m) cc_final: 0.8865 (t) REVERT: H 179 GLN cc_start: 0.9584 (tm-30) cc_final: 0.9361 (tm-30) REVERT: H 190 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8867 (tm-30) REVERT: I 134 ASP cc_start: 0.8413 (m-30) cc_final: 0.8078 (m-30) REVERT: I 143 ASP cc_start: 0.8594 (t70) cc_final: 0.7932 (t70) REVERT: I 147 GLN cc_start: 0.9592 (mm-40) cc_final: 0.9110 (mt0) REVERT: I 173 CYS cc_start: 0.9469 (m) cc_final: 0.8734 (t) REVERT: I 179 GLN cc_start: 0.9506 (tm-30) cc_final: 0.9206 (tm-30) REVERT: I 190 GLU cc_start: 0.9497 (mm-30) cc_final: 0.8209 (tp30) REVERT: I 193 GLU cc_start: 0.9053 (pp20) cc_final: 0.8001 (pp20) REVERT: I 194 ARG cc_start: 0.7471 (mtm110) cc_final: 0.7214 (mtm110) REVERT: J 114 PHE cc_start: 0.8395 (t80) cc_final: 0.7984 (t80) REVERT: J 117 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9114 (tm-30) REVERT: J 130 GLU cc_start: 0.7390 (pp20) cc_final: 0.6706 (pp20) REVERT: J 134 ASP cc_start: 0.8915 (m-30) cc_final: 0.7933 (m-30) REVERT: J 145 GLN cc_start: 0.9547 (mt0) cc_final: 0.9318 (mt0) REVERT: J 154 THR cc_start: 0.8139 (p) cc_final: 0.7683 (p) REVERT: J 158 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8434 (mtmm) REVERT: J 165 PHE cc_start: 0.9540 (m-10) cc_final: 0.9275 (m-10) REVERT: J 173 CYS cc_start: 0.9422 (m) cc_final: 0.8883 (t) REVERT: J 175 ASP cc_start: 0.9573 (t70) cc_final: 0.9264 (t0) REVERT: J 178 LEU cc_start: 0.9445 (tt) cc_final: 0.9081 (pp) REVERT: J 179 GLN cc_start: 0.9554 (tm-30) cc_final: 0.9323 (tm-30) REVERT: J 190 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8544 (tp30) REVERT: J 194 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7138 (mmm160) REVERT: K 112 LEU cc_start: 0.8976 (mt) cc_final: 0.8279 (mm) REVERT: K 114 PHE cc_start: 0.8437 (t80) cc_final: 0.8128 (t80) REVERT: K 117 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9129 (tm-30) REVERT: K 139 LYS cc_start: 0.9423 (mtmm) cc_final: 0.9105 (mtmm) REVERT: K 158 LYS cc_start: 0.9029 (mttp) cc_final: 0.8621 (mtmm) REVERT: K 160 ARG cc_start: 0.9135 (mtt180) cc_final: 0.8698 (mtt180) REVERT: K 164 SER cc_start: 0.9624 (p) cc_final: 0.9076 (p) REVERT: K 174 LYS cc_start: 0.9531 (mttt) cc_final: 0.9182 (ttmt) REVERT: K 179 GLN cc_start: 0.9495 (tm-30) cc_final: 0.9217 (tm-30) REVERT: K 190 GLU cc_start: 0.9003 (tp30) cc_final: 0.8181 (tp30) REVERT: K 193 GLU cc_start: 0.8524 (pp20) cc_final: 0.7746 (pp20) REVERT: L 116 ASP cc_start: 0.9199 (t70) cc_final: 0.8923 (t0) REVERT: L 134 ASP cc_start: 0.8934 (m-30) cc_final: 0.8340 (m-30) REVERT: L 174 LYS cc_start: 0.9484 (mttt) cc_final: 0.9097 (mttp) outliers start: 2 outliers final: 0 residues processed: 530 average time/residue: 0.1076 time to fit residues: 75.0768 Evaluate side-chains 440 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 145 GLN I 145 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.054687 restraints weight = 30373.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.056761 restraints weight = 16866.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.058155 restraints weight = 10849.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.059159 restraints weight = 7678.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.059938 restraints weight = 5675.234| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8448 Z= 0.132 Angle : 0.754 8.456 11472 Z= 0.357 Chirality : 0.043 0.228 1272 Planarity : 0.005 0.054 1452 Dihedral : 4.434 20.847 1092 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 972 helix: 1.37 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -2.32 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 194 TYR 0.019 0.002 TYR K 146 PHE 0.015 0.002 PHE E 163 TRP 0.022 0.001 TRP L 171 HIS 0.006 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8448) covalent geometry : angle 0.75374 (11472) hydrogen bonds : bond 0.02612 ( 504) hydrogen bonds : angle 3.88594 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 0.259 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: A 114 PHE cc_start: 0.8863 (t80) cc_final: 0.8572 (t80) REVERT: A 125 ARG cc_start: 0.9338 (tpp80) cc_final: 0.9008 (tpp80) REVERT: A 143 ASP cc_start: 0.9131 (t0) cc_final: 0.8034 (t70) REVERT: A 144 GLU cc_start: 0.9060 (pm20) cc_final: 0.8839 (pm20) REVERT: A 147 GLN cc_start: 0.9585 (mm-40) cc_final: 0.8896 (mp10) REVERT: A 158 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8808 (mtmm) REVERT: A 174 LYS cc_start: 0.9608 (mttt) cc_final: 0.9214 (mttp) REVERT: A 190 GLU cc_start: 0.9115 (tp30) cc_final: 0.8759 (tp30) REVERT: A 193 GLU cc_start: 0.8721 (pp20) cc_final: 0.8434 (pp20) REVERT: B 114 PHE cc_start: 0.8351 (t80) cc_final: 0.8117 (t80) REVERT: B 125 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8673 (mmm-85) REVERT: B 128 ASN cc_start: 0.8937 (t0) cc_final: 0.8194 (t0) REVERT: B 144 GLU cc_start: 0.9065 (pm20) cc_final: 0.8748 (pm20) REVERT: B 147 GLN cc_start: 0.9206 (mt0) cc_final: 0.8723 (mp10) REVERT: B 175 ASP cc_start: 0.9465 (t70) cc_final: 0.9192 (m-30) REVERT: B 179 GLN cc_start: 0.9605 (tm-30) cc_final: 0.9391 (tm-30) REVERT: B 190 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 191 ASP cc_start: 0.9076 (t0) cc_final: 0.8778 (t0) REVERT: C 134 ASP cc_start: 0.8782 (m-30) cc_final: 0.8493 (m-30) REVERT: C 143 ASP cc_start: 0.9227 (t70) cc_final: 0.8219 (t70) REVERT: C 147 GLN cc_start: 0.9718 (mm-40) cc_final: 0.8944 (mt0) REVERT: C 155 ASN cc_start: 0.8806 (m110) cc_final: 0.8553 (m-40) REVERT: C 158 LYS cc_start: 0.9288 (mtmm) cc_final: 0.8982 (mttp) REVERT: C 183 GLU cc_start: 0.9295 (tm-30) cc_final: 0.9065 (tm-30) REVERT: C 190 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8743 (tm-30) REVERT: C 191 ASP cc_start: 0.9205 (t70) cc_final: 0.8917 (t0) REVERT: D 117 GLN cc_start: 0.9421 (tp-100) cc_final: 0.9131 (tp-100) REVERT: D 134 ASP cc_start: 0.8475 (m-30) cc_final: 0.8184 (m-30) REVERT: D 139 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9122 (mppt) REVERT: D 147 GLN cc_start: 0.9333 (mt0) cc_final: 0.8810 (mt0) REVERT: D 154 THR cc_start: 0.8111 (p) cc_final: 0.7835 (p) REVERT: D 158 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8473 (mttp) REVERT: D 160 ARG cc_start: 0.9272 (mtt180) cc_final: 0.9057 (mtt180) REVERT: D 169 TRP cc_start: 0.9244 (m-10) cc_final: 0.8879 (m-10) REVERT: D 179 GLN cc_start: 0.9517 (tm-30) cc_final: 0.9257 (tm-30) REVERT: D 184 SER cc_start: 0.8843 (t) cc_final: 0.8463 (t) REVERT: D 193 GLU cc_start: 0.8578 (pm20) cc_final: 0.8168 (pm20) REVERT: E 114 PHE cc_start: 0.8441 (t80) cc_final: 0.8186 (t80) REVERT: E 117 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9109 (tm-30) REVERT: E 130 GLU cc_start: 0.8657 (pm20) cc_final: 0.8113 (pm20) REVERT: E 134 ASP cc_start: 0.9003 (m-30) cc_final: 0.8598 (m-30) REVERT: E 139 LYS cc_start: 0.9447 (mtmm) cc_final: 0.9152 (mtmm) REVERT: E 144 GLU cc_start: 0.8353 (tt0) cc_final: 0.8019 (tt0) REVERT: E 147 GLN cc_start: 0.9575 (mm-40) cc_final: 0.9233 (mt0) REVERT: E 158 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8787 (mtmm) REVERT: E 165 PHE cc_start: 0.8886 (m-10) cc_final: 0.8542 (m-10) REVERT: E 169 TRP cc_start: 0.9127 (m-10) cc_final: 0.8890 (m-10) REVERT: E 190 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8957 (tp30) REVERT: F 114 PHE cc_start: 0.8649 (t80) cc_final: 0.8431 (t80) REVERT: F 130 GLU cc_start: 0.8666 (pm20) cc_final: 0.8405 (pm20) REVERT: F 134 ASP cc_start: 0.8622 (m-30) cc_final: 0.8375 (m-30) REVERT: F 145 GLN cc_start: 0.9342 (mt0) cc_final: 0.8804 (mt0) REVERT: F 165 PHE cc_start: 0.9390 (m-80) cc_final: 0.9054 (m-80) REVERT: F 173 CYS cc_start: 0.9431 (m) cc_final: 0.8996 (t) REVERT: F 174 LYS cc_start: 0.9463 (mtmm) cc_final: 0.9101 (mtmm) REVERT: F 175 ASP cc_start: 0.9522 (t70) cc_final: 0.9229 (m-30) REVERT: F 179 GLN cc_start: 0.9586 (tm-30) cc_final: 0.9376 (tm-30) REVERT: G 117 GLN cc_start: 0.9464 (tm-30) cc_final: 0.9143 (tm-30) REVERT: G 129 VAL cc_start: 0.9501 (p) cc_final: 0.9259 (p) REVERT: G 130 GLU cc_start: 0.8307 (pm20) cc_final: 0.7963 (pm20) REVERT: G 143 ASP cc_start: 0.9180 (t70) cc_final: 0.8971 (t0) REVERT: G 158 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8878 (mtmm) REVERT: G 173 CYS cc_start: 0.9237 (m) cc_final: 0.8800 (t) REVERT: G 190 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8655 (tm-30) REVERT: H 114 PHE cc_start: 0.8913 (t80) cc_final: 0.8403 (t80) REVERT: H 117 GLN cc_start: 0.9544 (tm-30) cc_final: 0.9257 (tm-30) REVERT: H 134 ASP cc_start: 0.8909 (m-30) cc_final: 0.8609 (m-30) REVERT: H 158 LYS cc_start: 0.9199 (mttp) cc_final: 0.8926 (mttp) REVERT: H 173 CYS cc_start: 0.9478 (m) cc_final: 0.8808 (t) REVERT: H 174 LYS cc_start: 0.9535 (mttp) cc_final: 0.9195 (mtmm) REVERT: H 175 ASP cc_start: 0.9515 (t70) cc_final: 0.9292 (t0) REVERT: H 179 GLN cc_start: 0.9559 (tm-30) cc_final: 0.9349 (tm-30) REVERT: H 190 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8855 (tm-30) REVERT: I 134 ASP cc_start: 0.8351 (m-30) cc_final: 0.8014 (m-30) REVERT: I 143 ASP cc_start: 0.8540 (t70) cc_final: 0.7273 (t70) REVERT: I 144 GLU cc_start: 0.8909 (pp20) cc_final: 0.8616 (pp20) REVERT: I 147 GLN cc_start: 0.9567 (mm-40) cc_final: 0.8870 (mp10) REVERT: I 173 CYS cc_start: 0.9383 (m) cc_final: 0.8760 (t) REVERT: I 179 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9264 (tm-30) REVERT: I 190 GLU cc_start: 0.9461 (mm-30) cc_final: 0.8151 (tp30) REVERT: I 193 GLU cc_start: 0.8950 (pp20) cc_final: 0.7961 (pp20) REVERT: I 194 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7256 (mtm110) REVERT: J 114 PHE cc_start: 0.8318 (t80) cc_final: 0.7972 (t80) REVERT: J 117 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9187 (tm-30) REVERT: J 130 GLU cc_start: 0.7467 (pp20) cc_final: 0.6473 (pp20) REVERT: J 134 ASP cc_start: 0.8785 (m-30) cc_final: 0.7666 (m-30) REVERT: J 158 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8524 (mtmm) REVERT: J 173 CYS cc_start: 0.9316 (m) cc_final: 0.8870 (t) REVERT: J 174 LYS cc_start: 0.9405 (mttp) cc_final: 0.8988 (mppt) REVERT: J 175 ASP cc_start: 0.9530 (t70) cc_final: 0.9208 (t0) REVERT: J 178 LEU cc_start: 0.9513 (tt) cc_final: 0.9118 (pp) REVERT: J 179 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9284 (tm-30) REVERT: J 190 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8455 (tp30) REVERT: J 194 ARG cc_start: 0.7338 (mmm160) cc_final: 0.7117 (mmp80) REVERT: K 112 LEU cc_start: 0.8959 (mt) cc_final: 0.8268 (mm) REVERT: K 134 ASP cc_start: 0.8495 (m-30) cc_final: 0.8174 (m-30) REVERT: K 139 LYS cc_start: 0.9424 (mtmm) cc_final: 0.9144 (mtmm) REVERT: K 160 ARG cc_start: 0.8948 (mtt180) cc_final: 0.8567 (mtt180) REVERT: K 164 SER cc_start: 0.9635 (p) cc_final: 0.9141 (p) REVERT: K 173 CYS cc_start: 0.9367 (m) cc_final: 0.9160 (t) REVERT: K 174 LYS cc_start: 0.9530 (mttt) cc_final: 0.9211 (ttmt) REVERT: K 179 GLN cc_start: 0.9489 (tm-30) cc_final: 0.9190 (tm-30) REVERT: K 190 GLU cc_start: 0.8879 (tp30) cc_final: 0.8192 (tp30) REVERT: L 116 ASP cc_start: 0.9125 (t70) cc_final: 0.8846 (t0) REVERT: L 134 ASP cc_start: 0.8891 (m-30) cc_final: 0.8195 (m-30) REVERT: L 190 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8461 (tm-30) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.1040 time to fit residues: 70.4146 Evaluate side-chains 427 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 145 GLN I 145 GLN ** L 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.064049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.054850 restraints weight = 30764.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.056938 restraints weight = 16993.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.058375 restraints weight = 10909.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.059379 restraints weight = 7626.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.060151 restraints weight = 5679.502| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8448 Z= 0.134 Angle : 0.761 8.402 11472 Z= 0.363 Chirality : 0.043 0.257 1272 Planarity : 0.005 0.053 1452 Dihedral : 4.363 21.212 1092 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 972 helix: 1.35 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -2.24 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 194 TYR 0.019 0.002 TYR K 146 PHE 0.015 0.001 PHE K 165 TRP 0.019 0.001 TRP C 131 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8448) covalent geometry : angle 0.76098 (11472) hydrogen bonds : bond 0.02603 ( 504) hydrogen bonds : angle 3.97234 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.74 seconds wall clock time: 31 minutes 13.06 seconds (1873.06 seconds total)