Starting phenix.real_space_refine on Thu Aug 6 12:43:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8svf_40789/08_2026/8svf_40789.cif" } resolution = 3.2 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 25 5.16 5 C 8678 2.51 5 N 2835 2.21 5 O 3421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15254 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 753 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 669 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3138 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Chain: "J" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2909 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2122 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "L" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "M" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 438 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 3.36, per 1000 atoms: 0.22 Number of scatterers: 15254 At special positions: 0 Unit cell: (121.181, 142.256, 116.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 295 15.00 O 3421 8.00 N 2835 7.00 C 8678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 516.3 milliseconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 64.8% alpha, 5.9% beta 142 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.569A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.500A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.523A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.893A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.531A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.593A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.945A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.572A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.708A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.514A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.610A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.612A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 11 through 23 Processing helix chain 'K' and resid 36 through 40 removed outlier: 3.730A pdb=" N GLN K 40 " --> pdb=" O SER K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.697A pdb=" N ASN K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.867A pdb=" N LEU K 112 " --> pdb=" O LEU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 133 Processing helix chain 'K' and resid 134 through 143 Processing helix chain 'K' and resid 202 through 218 removed outlier: 3.759A pdb=" N ALA K 206 " --> pdb=" O TRP K 202 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL K 209 " --> pdb=" O LYS K 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR K 218 " --> pdb=" O ILE K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 244 Processing helix chain 'K' and resid 647 through 668 Processing helix chain 'K' and resid 671 through 686 Processing helix chain 'K' and resid 687 through 696 Processing helix chain 'L' and resid 257 through 262 Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 269 through 276 removed outlier: 3.683A pdb=" N LEU L 276 " --> pdb=" O THR L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 286 Processing helix chain 'L' and resid 310 through 327 Processing helix chain 'L' and resid 330 through 345 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.787A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.582A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.286A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.046A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.819A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.464A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 31 removed outlier: 4.558A pdb=" N GLY K 194 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU K 182 " --> pdb=" O ASP K 192 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP K 192 " --> pdb=" O GLU K 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 293 through 295 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 15 removed outlier: 6.404A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU M 43 " --> pdb=" O LEU M 50 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.75 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: 3041 1.33 - 1.45: 4844 1.45 - 1.57: 7608 1.57 - 1.69: 588 1.69 - 1.81: 43 Bond restraints: 16124 Sorted by residual: bond pdb=" C3' DC I 133 " pdb=" C2' DC I 133 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" N ASN K 695 " pdb=" CA ASN K 695 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" C3' DA I 37 " pdb=" C2' DA I 37 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I 129 " pdb=" C2' DC I 129 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA I 20 " pdb=" C2' DA I 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 16119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 20551 1.03 - 2.06: 1853 2.06 - 3.09: 619 3.09 - 4.13: 37 4.13 - 5.16: 9 Bond angle restraints: 23069 Sorted by residual: angle pdb=" N3 DT J 57 " pdb=" C4 DT J 57 " pdb=" O4 DT J 57 " ideal model delta sigma weight residual 119.90 122.79 -2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" O4' C I 19 " pdb=" C1' C I 19 " pdb=" N1 C I 19 " ideal model delta sigma weight residual 108.00 111.18 -3.18 7.00e-01 2.04e+00 2.06e+01 angle pdb=" O4' DA I 105 " pdb=" C4' DA I 105 " pdb=" C3' DA I 105 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I 83 " pdb=" C4 DT I 83 " pdb=" O4 DT I 83 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O4 DT J 57 " pdb=" C4 DT J 57 " pdb=" C5 DT J 57 " ideal model delta sigma weight residual 124.90 121.84 3.06 7.00e-01 2.04e+00 1.91e+01 ... (remaining 23064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 7549 35.09 - 70.19: 1333 70.19 - 105.28: 15 105.28 - 140.37: 0 140.37 - 175.47: 2 Dihedral angle restraints: 8899 sinusoidal: 5460 harmonic: 3439 Sorted by residual: dihedral pdb=" C4' DT I 153 " pdb=" C3' DT I 153 " pdb=" O3' DT I 153 " pdb=" P DC I 154 " ideal model delta sinusoidal sigma weight residual 220.00 44.53 175.47 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG I 119 " pdb=" C3' DG I 119 " pdb=" O3' DG I 119 " pdb=" P DG I 120 " ideal model delta sinusoidal sigma weight residual 220.00 69.83 150.17 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA TRP K 196 " pdb=" C TRP K 196 " pdb=" N GLY K 197 " pdb=" CA GLY K 197 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1859 0.041 - 0.081: 579 0.081 - 0.122: 190 0.122 - 0.162: 13 0.162 - 0.203: 2 Chirality restraints: 2643 Sorted by residual: chirality pdb=" CA ILE K 696 " pdb=" N ILE K 696 " pdb=" C ILE K 696 " pdb=" CB ILE K 696 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU K 691 " pdb=" N LEU K 691 " pdb=" C LEU K 691 " pdb=" CB LEU K 691 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" C3' DT I 153 " pdb=" C4' DT I 153 " pdb=" O3' DT I 153 " pdb=" C2' DT I 153 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 2640 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 146 " 0.025 2.00e-02 2.50e+03 1.09e-02 3.25e+00 pdb=" N9 DA I 146 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 146 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 146 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 146 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 146 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 146 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 146 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 146 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 146 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 146 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 135 " 0.023 2.00e-02 2.50e+03 9.97e-03 2.74e+00 pdb=" N9 DA I 135 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 135 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 135 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 135 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 135 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 135 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 135 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 135 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 135 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 254 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO L 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 255 " -0.023 5.00e-02 4.00e+02 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1967 2.76 - 3.29: 13781 3.29 - 3.83: 28727 3.83 - 4.36: 32449 4.36 - 4.90: 49531 Nonbonded interactions: 126455 Sorted by model distance: nonbonded pdb=" O PHE K 122 " pdb=" NZ LYS K 127 " model vdw 2.220 3.120 nonbonded pdb=" NE2 HIS K 169 " pdb=" OD1 ASP K 184 " model vdw 2.228 3.120 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.292 3.040 nonbonded pdb=" O ILE M 36 " pdb=" NE2 GLN M 41 " model vdw 2.315 3.120 nonbonded pdb=" O MET K 115 " pdb=" OG1 THR K 119 " model vdw 2.327 3.040 ... (remaining 126450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 110)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 110)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.005 0.042 16124 Z= 0.464 Angle : 0.680 5.156 23069 Z= 0.601 Chirality : 0.043 0.203 2643 Planarity : 0.003 0.041 1916 Dihedral : 24.962 175.468 6669 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 3.43 % Favored : 95.29 % 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: 2.82 (0.25), residues: 1159 helix: 2.90 (0.19), residues: 721 sheet: 1.29 (0.78), residues: 48 loop : -0.07 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 60 TYR 0.007 0.001 TYR G 57 PHE 0.009 0.001 PHE K 50 TRP 0.013 0.002 TRP K 52 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.46 (16124) covalent geometry : angle 0.68047 / 0.60 (23069) hydrogen bonds : bond 0.10976 / 7.39 ( 935) hydrogen bonds : angle 3.82475 / 2.85 ( 2385) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 0.273 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 79 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8156 (tttp) REVERT: A 107 THR cc_start: 0.9408 (m) cc_final: 0.9019 (p) REVERT: B 53 GLU cc_start: 0.8379 (tp30) cc_final: 0.8068 (tp30) REVERT: B 63 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 75 LYS cc_start: 0.9181 (mttm) cc_final: 0.8874 (mtpp) REVERT: C 90 ASP cc_start: 0.8826 (t0) cc_final: 0.8469 (t0) REVERT: E 90 MET cc_start: 0.9002 (mmp) cc_final: 0.8800 (mmm) REVERT: F 25 ASN cc_start: 0.8405 (m-40) cc_final: 0.8200 (m-40) REVERT: G 90 ASP cc_start: 0.8322 (t0) cc_final: 0.7136 (t0) REVERT: G 100 VAL cc_start: 0.9682 (t) cc_final: 0.9422 (p) REVERT: K 53 ILE cc_start: 0.4429 (OUTLIER) cc_final: 0.4087 (pp) REVERT: K 231 MET cc_start: 0.7609 (mtm) cc_final: 0.7028 (mtt) REVERT: L 262 THR cc_start: 0.9066 (m) cc_final: 0.8637 (t) REVERT: L 312 PHE cc_start: 0.9043 (m-80) cc_final: 0.8406 (m-80) REVERT: L 321 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8819 (ptm160) REVERT: L 334 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8381 (mm-40) REVERT: L 336 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8260 (tmt170) outliers start: 12 outliers final: 4 residues processed: 271 average time/residue: 0.1432 time to fit residues: 53.3304 Evaluate side-chains 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 81 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 24 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.092715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.058903 restraints weight = 55488.445| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.24 r_work: 0.2961 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16124 Z= 0.193 Angle : 0.625 9.799 23069 Z= 0.364 Chirality : 0.044 0.291 2643 Planarity : 0.005 0.042 1916 Dihedral : 29.291 176.911 4528 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.25 % Allowed : 9.64 % Favored : 88.12 % 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: 2.60 (0.24), residues: 1159 helix: 2.68 (0.19), residues: 738 sheet: 0.86 (0.74), residues: 48 loop : -0.14 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.014 0.001 TYR F 51 PHE 0.018 0.001 PHE L 280 TRP 0.012 0.002 TRP K 52 HIS 0.007 0.002 HIS K 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (16124) covalent geometry : angle 0.62537 / 0.36 (23069) hydrogen bonds : bond 0.05094 / 3.42 ( 935) hydrogen bonds : angle 3.23190 / 2.40 ( 2385) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.303 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 42 ARG cc_start: 0.7593 (mtp85) cc_final: 0.7102 (mpt180) REVERT: A 79 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8208 (tttp) REVERT: A 94 GLU cc_start: 0.8534 (tp30) cc_final: 0.8332 (tp30) REVERT: A 107 THR cc_start: 0.9434 (m) cc_final: 0.9046 (p) REVERT: B 49 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9124 (mm) REVERT: B 53 GLU cc_start: 0.8915 (tp30) cc_final: 0.8618 (tp30) REVERT: B 63 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8235 (mt-10) REVERT: C 64 GLU cc_start: 0.9141 (tt0) cc_final: 0.8828 (tm-30) REVERT: C 75 LYS cc_start: 0.9183 (mttm) cc_final: 0.8908 (mtpp) REVERT: C 90 ASP cc_start: 0.9008 (t0) cc_final: 0.8653 (t0) REVERT: C 95 LYS cc_start: 0.9383 (ttmm) cc_final: 0.9173 (ttmm) REVERT: F 25 ASN cc_start: 0.8878 (m-40) cc_final: 0.8626 (m-40) REVERT: F 63 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8026 (tm-30) REVERT: F 74 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8755 (mt-10) REVERT: G 90 ASP cc_start: 0.8197 (t0) cc_final: 0.7564 (t0) REVERT: G 100 VAL cc_start: 0.9746 (t) cc_final: 0.9480 (p) REVERT: H 68 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8865 (tp30) REVERT: H 102 GLU cc_start: 0.8335 (mp0) cc_final: 0.7902 (tt0) REVERT: K 231 MET cc_start: 0.8054 (mtm) cc_final: 0.7348 (mtt) REVERT: K 695 ASN cc_start: 0.8544 (t0) cc_final: 0.8232 (t0) REVERT: L 251 ASP cc_start: 0.5869 (t0) cc_final: 0.5318 (t0) REVERT: L 286 PHE cc_start: 0.8885 (m-10) cc_final: 0.8499 (t80) REVERT: L 312 PHE cc_start: 0.9059 (m-80) cc_final: 0.8602 (m-80) REVERT: L 334 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8412 (mm-40) REVERT: L 336 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8168 (tmt170) outliers start: 21 outliers final: 16 residues processed: 206 average time/residue: 0.1215 time to fit residues: 35.5572 Evaluate side-chains 193 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.092571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059061 restraints weight = 56181.152| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.24 r_work: 0.2994 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16124 Z= 0.142 Angle : 0.567 8.396 23069 Z= 0.335 Chirality : 0.042 0.288 2643 Planarity : 0.004 0.042 1916 Dihedral : 29.337 177.677 4526 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.25 % Allowed : 10.39 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.24), residues: 1159 helix: 2.88 (0.19), residues: 730 sheet: 0.73 (0.74), residues: 48 loop : -0.18 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.019 0.001 TYR B 88 PHE 0.010 0.001 PHE L 280 TRP 0.014 0.001 TRP K 52 HIS 0.013 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (16124) covalent geometry : angle 0.56688 / 0.34 (23069) hydrogen bonds : bond 0.04391 / 2.95 ( 935) hydrogen bonds : angle 2.99033 / 2.21 ( 2385) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7058 (mpt180) REVERT: A 79 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8192 (tttp) REVERT: A 107 THR cc_start: 0.9421 (m) cc_final: 0.9024 (p) REVERT: B 49 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 63 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8286 (mt-10) REVERT: B 84 MET cc_start: 0.8764 (mmm) cc_final: 0.8199 (mmm) REVERT: B 88 TYR cc_start: 0.9059 (m-10) cc_final: 0.8730 (m-10) REVERT: C 64 GLU cc_start: 0.9170 (tt0) cc_final: 0.8881 (tm-30) REVERT: C 90 ASP cc_start: 0.9028 (t0) cc_final: 0.8676 (t0) REVERT: C 91 GLU cc_start: 0.8772 (tp30) cc_final: 0.8429 (tp30) REVERT: C 95 LYS cc_start: 0.9429 (ttmm) cc_final: 0.9110 (ttmm) REVERT: F 25 ASN cc_start: 0.8876 (m-40) cc_final: 0.8219 (m110) REVERT: F 63 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8113 (tm-30) REVERT: G 38 ASN cc_start: 0.9212 (m-40) cc_final: 0.8871 (p0) REVERT: G 90 ASP cc_start: 0.8214 (t0) cc_final: 0.7525 (t0) REVERT: G 92 GLU cc_start: 0.8494 (pm20) cc_final: 0.8213 (pm20) REVERT: G 100 VAL cc_start: 0.9749 (t) cc_final: 0.9482 (p) REVERT: H 68 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8894 (tp30) REVERT: K 231 MET cc_start: 0.8025 (mtm) cc_final: 0.7303 (mtt) REVERT: K 695 ASN cc_start: 0.8499 (t0) cc_final: 0.8171 (t0) REVERT: L 251 ASP cc_start: 0.6222 (t0) cc_final: 0.6022 (t0) REVERT: L 286 PHE cc_start: 0.8861 (m-10) cc_final: 0.8461 (t80) REVERT: L 334 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8342 (mm-40) REVERT: L 336 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8140 (tmt170) outliers start: 21 outliers final: 14 residues processed: 196 average time/residue: 0.1136 time to fit residues: 32.1208 Evaluate side-chains 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 30 optimal weight: 1.9990 chunk 118 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 169 HIS ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.091133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057246 restraints weight = 55989.897| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.21 r_work: 0.2940 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16124 Z= 0.216 Angle : 0.648 8.598 23069 Z= 0.362 Chirality : 0.044 0.287 2643 Planarity : 0.005 0.047 1916 Dihedral : 29.557 178.377 4522 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.36 % Allowed : 11.56 % Favored : 86.08 % 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: 2.50 (0.24), residues: 1159 helix: 2.68 (0.19), residues: 736 sheet: 0.42 (0.73), residues: 48 loop : -0.29 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.018 0.002 TYR K 241 PHE 0.014 0.002 PHE K 170 TRP 0.015 0.001 TRP K 52 HIS 0.010 0.002 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (16124) covalent geometry : angle 0.64842 / 0.36 (23069) hydrogen bonds : bond 0.05233 / 3.52 ( 935) hydrogen bonds : angle 3.22787 / 2.39 ( 2385) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.379 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 79 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8347 (tttp) REVERT: A 125 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8776 (mm-40) REVERT: B 63 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8379 (mt-10) REVERT: C 64 GLU cc_start: 0.9214 (tt0) cc_final: 0.8956 (tm-30) REVERT: C 90 ASP cc_start: 0.9079 (t0) cc_final: 0.8755 (t0) REVERT: C 91 GLU cc_start: 0.8835 (tp30) cc_final: 0.8485 (tp30) REVERT: C 95 LYS cc_start: 0.9430 (ttmm) cc_final: 0.9094 (ttmm) REVERT: D 79 HIS cc_start: 0.9150 (t-90) cc_final: 0.8928 (t-90) REVERT: F 25 ASN cc_start: 0.8801 (m-40) cc_final: 0.8140 (m110) REVERT: F 63 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8305 (tm-30) REVERT: G 90 ASP cc_start: 0.8177 (t0) cc_final: 0.7363 (t0) REVERT: G 100 VAL cc_start: 0.9760 (t) cc_final: 0.9469 (p) REVERT: H 68 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8922 (tp30) REVERT: K 231 MET cc_start: 0.7952 (mtm) cc_final: 0.7318 (mtt) REVERT: K 695 ASN cc_start: 0.8611 (t0) cc_final: 0.8236 (t0) REVERT: L 251 ASP cc_start: 0.6373 (t0) cc_final: 0.5828 (t0) REVERT: L 286 PHE cc_start: 0.8876 (m-10) cc_final: 0.8486 (t80) REVERT: L 334 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8342 (mm-40) REVERT: L 336 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8198 (tmt170) outliers start: 22 outliers final: 16 residues processed: 193 average time/residue: 0.1069 time to fit residues: 30.1734 Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.091959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.058222 restraints weight = 55895.161| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.21 r_work: 0.2954 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16124 Z= 0.147 Angle : 0.584 7.054 23069 Z= 0.336 Chirality : 0.043 0.293 2643 Planarity : 0.004 0.041 1916 Dihedral : 29.483 178.446 4522 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.25 % Allowed : 13.06 % Favored : 84.69 % 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: 2.65 (0.24), residues: 1159 helix: 2.80 (0.19), residues: 735 sheet: 0.49 (0.75), residues: 48 loop : -0.22 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.026 0.002 TYR B 88 PHE 0.029 0.001 PHE L 252 TRP 0.013 0.001 TRP K 52 HIS 0.009 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (16124) covalent geometry : angle 0.58388 / 0.34 (23069) hydrogen bonds : bond 0.04448 / 2.99 ( 935) hydrogen bonds : angle 3.00348 / 2.23 ( 2385) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8316 (tttp) REVERT: A 125 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8764 (mm-40) REVERT: B 53 GLU cc_start: 0.8523 (tp30) cc_final: 0.8176 (tp30) REVERT: B 63 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 84 MET cc_start: 0.8854 (mmm) cc_final: 0.8331 (mmm) REVERT: B 88 TYR cc_start: 0.9068 (m-10) cc_final: 0.8703 (m-10) REVERT: C 64 GLU cc_start: 0.9219 (tt0) cc_final: 0.8903 (tm-30) REVERT: C 90 ASP cc_start: 0.9063 (t0) cc_final: 0.8732 (t0) REVERT: C 91 GLU cc_start: 0.8809 (tp30) cc_final: 0.8455 (tp30) REVERT: C 92 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8104 (tp30) REVERT: C 95 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9081 (ttmm) REVERT: F 25 ASN cc_start: 0.8786 (m-40) cc_final: 0.8143 (m110) REVERT: F 63 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8223 (tm-30) REVERT: F 74 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8755 (mt-10) REVERT: G 90 ASP cc_start: 0.8201 (t0) cc_final: 0.7573 (t0) REVERT: G 92 GLU cc_start: 0.8540 (pm20) cc_final: 0.8242 (pm20) REVERT: G 100 VAL cc_start: 0.9761 (t) cc_final: 0.9477 (p) REVERT: H 68 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8948 (tp30) REVERT: K 231 MET cc_start: 0.7883 (mtm) cc_final: 0.7308 (mtt) REVERT: K 695 ASN cc_start: 0.8525 (t0) cc_final: 0.8069 (t0) REVERT: L 251 ASP cc_start: 0.6056 (t0) cc_final: 0.5733 (t0) REVERT: L 334 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8322 (mm-40) REVERT: L 336 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8204 (tmt170) outliers start: 21 outliers final: 17 residues processed: 191 average time/residue: 0.1081 time to fit residues: 30.3035 Evaluate side-chains 186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 687 MET Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 2 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN K 169 HIS ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.091837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058254 restraints weight = 55385.617| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.21 r_work: 0.2975 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16124 Z= 0.132 Angle : 0.573 6.210 23069 Z= 0.332 Chirality : 0.042 0.295 2643 Planarity : 0.004 0.042 1916 Dihedral : 29.421 179.156 4522 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.36 % Allowed : 13.92 % Favored : 83.73 % 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: 2.77 (0.24), residues: 1159 helix: 2.90 (0.19), residues: 734 sheet: 0.52 (0.76), residues: 48 loop : -0.18 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.020 0.001 TYR B 88 PHE 0.010 0.001 PHE K 50 TRP 0.014 0.001 TRP K 52 HIS 0.016 0.001 HIS L 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (16124) covalent geometry : angle 0.57262 / 0.33 (23069) hydrogen bonds : bond 0.04129 / 2.77 ( 935) hydrogen bonds : angle 2.91454 / 2.16 ( 2385) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.325 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 79 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8272 (tttp) REVERT: A 125 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8777 (mm-40) REVERT: B 53 GLU cc_start: 0.8488 (tp30) cc_final: 0.8134 (tp30) REVERT: B 63 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 84 MET cc_start: 0.8930 (mmm) cc_final: 0.8353 (mmm) REVERT: B 88 TYR cc_start: 0.9072 (m-10) cc_final: 0.8715 (m-10) REVERT: C 64 GLU cc_start: 0.9218 (tt0) cc_final: 0.8903 (tm-30) REVERT: C 90 ASP cc_start: 0.9050 (t0) cc_final: 0.8711 (t0) REVERT: C 91 GLU cc_start: 0.8827 (tp30) cc_final: 0.8463 (tp30) REVERT: C 92 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8110 (tp30) REVERT: C 95 LYS cc_start: 0.9444 (ttmm) cc_final: 0.9084 (ttmm) REVERT: F 25 ASN cc_start: 0.8736 (m-40) cc_final: 0.8122 (m110) REVERT: F 63 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8174 (tm-30) REVERT: G 90 ASP cc_start: 0.8162 (t0) cc_final: 0.7505 (t0) REVERT: G 100 VAL cc_start: 0.9756 (t) cc_final: 0.9471 (p) REVERT: H 68 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8953 (tp30) REVERT: K 231 MET cc_start: 0.7893 (mtm) cc_final: 0.7327 (mtt) REVERT: K 695 ASN cc_start: 0.8473 (t0) cc_final: 0.7900 (m110) REVERT: L 334 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8327 (mm-40) REVERT: L 336 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8177 (tmt170) outliers start: 22 outliers final: 15 residues processed: 190 average time/residue: 0.1069 time to fit residues: 29.9995 Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 128 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056735 restraints weight = 55023.981| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.17 r_work: 0.2914 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16124 Z= 0.234 Angle : 0.671 7.351 23069 Z= 0.373 Chirality : 0.045 0.285 2643 Planarity : 0.004 0.041 1916 Dihedral : 29.685 179.577 4521 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.00 % Allowed : 13.60 % Favored : 83.40 % 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: 2.50 (0.25), residues: 1159 helix: 2.69 (0.19), residues: 729 sheet: 0.44 (0.76), residues: 48 loop : -0.26 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.024 0.002 TYR B 88 PHE 0.016 0.002 PHE A 67 TRP 0.017 0.002 TRP K 52 HIS 0.013 0.002 HIS L 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (16124) covalent geometry : angle 0.67053 / 0.37 (23069) hydrogen bonds : bond 0.05236 / 3.51 ( 935) hydrogen bonds : angle 3.25684 / 2.40 ( 2385) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.9062 (mmt90) REVERT: B 63 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8383 (mt-10) REVERT: C 56 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8851 (tm-30) REVERT: C 64 GLU cc_start: 0.9219 (tt0) cc_final: 0.8973 (tm-30) REVERT: C 90 ASP cc_start: 0.9117 (t0) cc_final: 0.8761 (t0) REVERT: C 91 GLU cc_start: 0.8863 (tp30) cc_final: 0.8509 (tp30) REVERT: C 95 LYS cc_start: 0.9422 (ttmm) cc_final: 0.9081 (ttmm) REVERT: F 25 ASN cc_start: 0.8682 (m-40) cc_final: 0.8060 (m110) REVERT: F 63 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8316 (tm-30) REVERT: G 90 ASP cc_start: 0.8265 (t0) cc_final: 0.7528 (t0) REVERT: G 92 GLU cc_start: 0.8517 (pm20) cc_final: 0.8083 (pm20) REVERT: G 100 VAL cc_start: 0.9765 (t) cc_final: 0.9465 (p) REVERT: H 68 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8928 (tp30) REVERT: K 231 MET cc_start: 0.7946 (mtm) cc_final: 0.7359 (mtt) REVERT: L 323 ARG cc_start: 0.9515 (mtp180) cc_final: 0.9181 (ttp-110) REVERT: L 334 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8339 (mm-40) REVERT: L 336 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8215 (tmt170) outliers start: 28 outliers final: 16 residues processed: 183 average time/residue: 0.1059 time to fit residues: 28.4758 Evaluate side-chains 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.091720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058137 restraints weight = 55780.531| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.24 r_work: 0.2953 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16124 Z= 0.133 Angle : 0.597 9.005 23069 Z= 0.342 Chirality : 0.042 0.295 2643 Planarity : 0.004 0.042 1916 Dihedral : 29.521 179.581 4521 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.71 % Allowed : 15.42 % Favored : 82.87 % 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: 2.70 (0.25), residues: 1159 helix: 2.88 (0.19), residues: 729 sheet: 0.51 (0.75), residues: 48 loop : -0.24 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.022 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.013 0.001 TRP K 52 HIS 0.013 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (16124) covalent geometry : angle 0.59715 / 0.34 (23069) hydrogen bonds : bond 0.04167 / 2.80 ( 935) hydrogen bonds : angle 2.93636 / 2.17 ( 2385) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 84 MET cc_start: 0.8883 (mmm) cc_final: 0.8666 (mmm) REVERT: B 88 TYR cc_start: 0.8979 (m-10) cc_final: 0.8659 (m-10) REVERT: C 56 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8786 (tm-30) REVERT: C 64 GLU cc_start: 0.9216 (tt0) cc_final: 0.8980 (tm-30) REVERT: C 90 ASP cc_start: 0.9059 (t0) cc_final: 0.8742 (t0) REVERT: C 91 GLU cc_start: 0.8838 (tp30) cc_final: 0.8479 (tp30) REVERT: C 92 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8104 (tp30) REVERT: C 95 LYS cc_start: 0.9440 (ttmm) cc_final: 0.9083 (ttmm) REVERT: D 80 TYR cc_start: 0.8172 (m-10) cc_final: 0.7697 (m-10) REVERT: F 25 ASN cc_start: 0.8739 (m-40) cc_final: 0.8133 (m110) REVERT: F 63 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 90 ASP cc_start: 0.8148 (t0) cc_final: 0.7743 (t0) REVERT: G 100 VAL cc_start: 0.9760 (t) cc_final: 0.9478 (p) REVERT: H 68 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8914 (tp30) REVERT: K 226 ILE cc_start: 0.0594 (OUTLIER) cc_final: 0.0171 (tt) REVERT: K 231 MET cc_start: 0.7928 (mtm) cc_final: 0.7373 (mtt) REVERT: L 251 ASP cc_start: 0.7290 (t0) cc_final: 0.7020 (t0) REVERT: L 334 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8349 (mm110) REVERT: L 336 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8204 (tmt170) outliers start: 16 outliers final: 11 residues processed: 183 average time/residue: 0.1153 time to fit residues: 30.9187 Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 106 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS M 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.091904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058326 restraints weight = 55542.183| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.22 r_work: 0.2967 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16124 Z= 0.132 Angle : 0.591 9.279 23069 Z= 0.341 Chirality : 0.042 0.294 2643 Planarity : 0.004 0.075 1916 Dihedral : 29.478 179.873 4521 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.50 % Allowed : 15.63 % Favored : 82.87 % 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: 2.61 (0.25), residues: 1159 helix: 2.83 (0.19), residues: 729 sheet: 0.20 (0.74), residues: 48 loop : -0.31 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 131 TYR 0.028 0.001 TYR B 88 PHE 0.009 0.001 PHE A 67 TRP 0.014 0.001 TRP K 52 HIS 0.022 0.002 HIS L 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (16124) covalent geometry : angle 0.59134 / 0.34 (23069) hydrogen bonds : bond 0.04032 / 2.71 ( 935) hydrogen bonds : angle 2.92845 / 2.16 ( 2385) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 88 TYR cc_start: 0.9001 (m-10) cc_final: 0.8660 (m-10) REVERT: B 92 ARG cc_start: 0.9324 (ttp80) cc_final: 0.9037 (ttp80) REVERT: C 56 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8714 (tm-30) REVERT: C 64 GLU cc_start: 0.9216 (tt0) cc_final: 0.9005 (tm-30) REVERT: C 90 ASP cc_start: 0.9078 (t0) cc_final: 0.8739 (t0) REVERT: C 91 GLU cc_start: 0.8836 (tp30) cc_final: 0.8453 (tp30) REVERT: C 92 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8123 (tp30) REVERT: C 95 LYS cc_start: 0.9445 (ttmm) cc_final: 0.9092 (ttmm) REVERT: D 80 TYR cc_start: 0.8121 (m-10) cc_final: 0.7647 (m-10) REVERT: F 25 ASN cc_start: 0.8696 (m-40) cc_final: 0.8115 (m110) REVERT: F 63 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8181 (tm-30) REVERT: G 90 ASP cc_start: 0.8196 (t0) cc_final: 0.7697 (t0) REVERT: G 92 GLU cc_start: 0.8461 (pm20) cc_final: 0.8160 (pm20) REVERT: G 100 VAL cc_start: 0.9760 (t) cc_final: 0.9470 (p) REVERT: H 68 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8909 (tp30) REVERT: K 226 ILE cc_start: 0.0564 (OUTLIER) cc_final: 0.0136 (tt) REVERT: K 231 MET cc_start: 0.7986 (mtm) cc_final: 0.7378 (mtt) REVERT: L 251 ASP cc_start: 0.7409 (t0) cc_final: 0.7190 (t0) REVERT: L 321 ARG cc_start: 0.8335 (ptm160) cc_final: 0.8132 (ptm160) REVERT: L 334 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8435 (mm-40) REVERT: L 336 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.8222 (tmt170) outliers start: 14 outliers final: 12 residues processed: 174 average time/residue: 0.1188 time to fit residues: 30.6618 Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** K 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.092076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.058552 restraints weight = 56151.573| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.24 r_work: 0.2982 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16124 Z= 0.132 Angle : 0.603 9.417 23069 Z= 0.345 Chirality : 0.041 0.293 2643 Planarity : 0.004 0.060 1916 Dihedral : 29.461 179.467 4521 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.50 % Allowed : 15.85 % Favored : 82.66 % 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: 2.59 (0.25), residues: 1159 helix: 2.83 (0.19), residues: 729 sheet: 0.14 (0.74), residues: 48 loop : -0.33 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 131 TYR 0.029 0.001 TYR B 88 PHE 0.009 0.001 PHE K 50 TRP 0.014 0.001 TRP K 52 HIS 0.015 0.001 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (16124) covalent geometry : angle 0.60290 / 0.35 (23069) hydrogen bonds : bond 0.03928 / 2.63 ( 935) hydrogen bonds : angle 2.95228 / 2.16 ( 2385) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8358 (mt-10) REVERT: B 84 MET cc_start: 0.8857 (mmm) cc_final: 0.8533 (mmm) REVERT: B 88 TYR cc_start: 0.8992 (m-10) cc_final: 0.8465 (m-10) REVERT: B 92 ARG cc_start: 0.9328 (ttp80) cc_final: 0.9041 (ttp80) REVERT: C 56 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8710 (tm-30) REVERT: C 90 ASP cc_start: 0.9068 (t0) cc_final: 0.8728 (t0) REVERT: C 91 GLU cc_start: 0.8828 (tp30) cc_final: 0.8447 (tp30) REVERT: C 92 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8123 (tp30) REVERT: C 95 LYS cc_start: 0.9434 (ttmm) cc_final: 0.9070 (ttmm) REVERT: D 80 TYR cc_start: 0.8060 (m-10) cc_final: 0.7788 (m-10) REVERT: F 25 ASN cc_start: 0.8692 (m-40) cc_final: 0.8143 (m110) REVERT: F 63 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 90 ASP cc_start: 0.8160 (t0) cc_final: 0.7687 (t0) REVERT: G 100 VAL cc_start: 0.9764 (t) cc_final: 0.9475 (p) REVERT: H 68 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8917 (tp30) REVERT: K 226 ILE cc_start: 0.0593 (OUTLIER) cc_final: 0.0159 (tt) REVERT: K 231 MET cc_start: 0.7967 (mtm) cc_final: 0.7344 (mtt) REVERT: L 334 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8414 (mm-40) REVERT: L 336 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8195 (tmt170) outliers start: 14 outliers final: 11 residues processed: 178 average time/residue: 0.1132 time to fit residues: 30.0444 Evaluate side-chains 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 664 ASP Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 7.9990 chunk 125 optimal weight: 0.0020 chunk 104 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 169 HIS ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS ** M 41 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 = 0.3982 r_free = 0.3982 target = 0.090530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056648 restraints weight = 55729.880| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.20 r_work: 0.2922 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16124 Z= 0.233 Angle : 0.670 8.602 23069 Z= 0.372 Chirality : 0.045 0.285 2643 Planarity : 0.004 0.046 1916 Dihedral : 29.667 179.236 4521 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.82 % Allowed : 15.85 % Favored : 82.33 % 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: 2.45 (0.25), residues: 1159 helix: 2.72 (0.19), residues: 729 sheet: 0.18 (0.73), residues: 48 loop : -0.40 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 131 TYR 0.039 0.002 TYR B 88 PHE 0.011 0.001 PHE G 25 TRP 0.018 0.002 TRP K 52 HIS 0.015 0.002 HIS K 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (16124) covalent geometry : angle 0.67032 / 0.37 (23069) hydrogen bonds : bond 0.04851 / 3.25 ( 935) hydrogen bonds : angle 3.18118 / 2.35 ( 2385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.39 seconds wall clock time: 75 minutes 23.47 seconds (4523.47 seconds total)