Starting phenix.real_space_refine on Sun Sep 13 05:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e9c_31029/09_2026/7e9c_31029.cif" } resolution = 3.5 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= 0.008 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11439 atoms to isotropic. 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 260 5.49 5 S 3 5.16 5 C 6945 2.51 5 N 2302 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2652 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "J" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2678 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "K" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1204 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'AYA:plan-2': 1, 'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 2.62, per 1000 atoms: 0.21 Number of scatterers: 12338 At special positions: 0 Unit cell: (116, 117, 111, 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 3 16.00 P 260 15.00 O 2828 8.00 N 2302 7.00 C 6945 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: 1.01 Conformation dependent library (CDL) restraints added in 386.9 milliseconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 61.6% alpha, 6.1% beta 116 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.976A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.513A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 53 through 76 removed outlier: 3.656A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.661A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.176A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.522A pdb=" N LYS C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 4.037A pdb=" N THR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.673A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.964A pdb=" N LYS D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 removed outlier: 4.130A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.879A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.506A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.563A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.086A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.420A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.917A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.383A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.552A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 98 removed outlier: 3.898A pdb=" N LEU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 93 through 98' Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.881A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.608A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 107 through 125 removed outlier: 3.810A pdb=" N LYS H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 199 removed outlier: 4.219A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 212 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.332A 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 removed outlier: 4.112A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.251A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.853A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.463A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 14 through 16 removed outlier: 4.257A pdb=" N LEU K 41 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 138 through 141 removed outlier: 4.187A pdb=" N LEU K 85 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 57 " --> pdb=" O ARG K 148 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG K 148 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS K 59 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE K 146 " --> pdb=" O HIS K 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 131 through 134 removed outlier: 7.524A pdb=" N LEU K 132 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE K 176 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU K 134 " --> pdb=" O ILE K 176 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET K 153 " --> pdb=" O VAL K 173 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N TYR K 175 " --> pdb=" O MET K 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 389 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 301 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2508 1.33 - 1.45: 4019 1.45 - 1.57: 6024 1.57 - 1.69: 518 1.69 - 1.81: 5 Bond restraints: 13074 Sorted by residual: bond pdb=" C3' DA I 52 " pdb=" C2' DA I 52 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA J 117 " pdb=" C2' DA J 117 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT J 45 " pdb=" C2' DT J 45 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG I 71 " pdb=" C2' DG I 71 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.69e+00 ... (remaining 13069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 17772 1.64 - 3.29: 939 3.29 - 4.93: 59 4.93 - 6.57: 12 6.57 - 8.22: 2 Bond angle restraints: 18784 Sorted by residual: angle pdb=" O4' DG I 34 " pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" O4' DA I 5 " pdb=" C4' DA I 5 " pdb=" C3' DA I 5 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT I 105 " pdb=" C4 DT I 105 " pdb=" O4 DT I 105 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.14e+01 angle pdb=" O4' DA J 113 " pdb=" C4' DA J 113 " pdb=" C3' DA J 113 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" O4 DT I 105 " pdb=" C4 DT I 105 " pdb=" C5 DT I 105 " ideal model delta sigma weight residual 124.90 121.85 3.05 7.00e-01 2.04e+00 1.90e+01 ... (remaining 18779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 5644 29.14 - 58.29: 1366 58.29 - 87.43: 144 87.43 - 116.57: 3 116.57 - 145.72: 2 Dihedral angle restraints: 7159 sinusoidal: 4551 harmonic: 2608 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 74.28 145.72 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 75.24 144.76 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1670 0.047 - 0.094: 417 0.094 - 0.141: 73 0.141 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU A 48 " pdb=" CB LEU A 48 " pdb=" CD1 LEU A 48 " pdb=" CD2 LEU A 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA GLN K 205 " pdb=" N GLN K 205 " pdb=" C GLN K 205 " pdb=" CB GLN K 205 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 2161 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 136 " -0.005 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG J 136 " 0.004 2.00e-02 2.50e+03 pdb=" C8 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 136 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J 136 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG J 136 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 136 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG J 136 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 136 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG J 136 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 136 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 32 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 105 " -0.020 2.00e-02 2.50e+03 1.03e-02 2.63e+00 pdb=" N1 DT I 105 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 105 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 105 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 105 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 105 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 105 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 105 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 105 " 0.000 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1614 2.76 - 3.29: 11701 3.29 - 3.83: 23832 3.83 - 4.36: 25834 4.36 - 4.90: 38608 Nonbonded interactions: 101589 Sorted by model distance: nonbonded pdb=" OD1 ASN K 21 " pdb=" OH TYR K 40 " model vdw 2.221 3.040 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR K 78 " pdb=" O ASN K 81 " model vdw 2.232 3.040 nonbonded pdb=" N4 DC I 64 " pdb=" N6 DA I 65 " model vdw 2.236 3.200 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.280 3.040 ... (remaining 101584 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 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 0.047 13074 Z= 0.468 Angle : 0.739 8.215 18784 Z= 0.644 Chirality : 0.042 0.236 2164 Planarity : 0.003 0.043 1475 Dihedral : 26.936 145.718 5471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 875 helix: 1.26 (0.23), residues: 518 sheet: -0.56 (0.99), residues: 29 loop : -1.76 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 52 TYR 0.016 0.001 TYR D 45 PHE 0.025 0.001 PHE H 73 TRP 0.003 0.001 TRP K 86 HIS 0.007 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.47 (13074) covalent geometry : angle 0.73941 / 0.64 (18784) hydrogen bonds : bond 0.11540 / 7.80 ( 690) hydrogen bonds : angle 4.89669 / 3.59 ( 1753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7910 (pm20) cc_final: 0.7513 (pm20) REVERT: B 83 SER cc_start: 0.8215 (t) cc_final: 0.7960 (t) REVERT: B 98 TYR cc_start: 0.7617 (m-10) cc_final: 0.7384 (m-10) REVERT: C 34 LEU cc_start: 0.8841 (tp) cc_final: 0.8631 (tp) REVERT: C 82 ARG cc_start: 0.8508 (tpt90) cc_final: 0.7864 (tpt90) REVERT: D 46 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8013 (mtpt) REVERT: D 71 ASP cc_start: 0.8258 (t70) cc_final: 0.7830 (t0) REVERT: E 130 LEU cc_start: 0.8284 (tp) cc_final: 0.7943 (tp) REVERT: F 52 GLU cc_start: 0.7666 (tp30) cc_final: 0.7422 (mm-30) REVERT: G 37 ARG cc_start: 0.7496 (mmp80) cc_final: 0.6440 (mtm-85) REVERT: G 57 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7529 (tm-30) REVERT: G 65 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7389 (tm-30) REVERT: H 71 ASP cc_start: 0.7979 (t70) cc_final: 0.7486 (t0) REVERT: H 79 GLU cc_start: 0.8357 (tp30) cc_final: 0.7946 (tp30) REVERT: H 111 LYS cc_start: 0.8181 (tmmt) cc_final: 0.7913 (tmtt) REVERT: K 13 ILE cc_start: 0.4961 (mt) cc_final: 0.4726 (pt) REVERT: K 52 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.6795 (ttp-170) REVERT: K 75 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6642 (mtm180) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1372 time to fit residues: 37.8845 Evaluate side-chains 159 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN E 55 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.139706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.102564 restraints weight = 37254.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.105885 restraints weight = 17625.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.108007 restraints weight = 11592.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.109240 restraints weight = 9284.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.109840 restraints weight = 8299.772| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13074 Z= 0.158 Angle : 0.603 7.343 18784 Z= 0.361 Chirality : 0.044 0.218 2164 Planarity : 0.004 0.035 1475 Dihedral : 30.381 148.271 3811 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.77 % Allowed : 14.25 % Favored : 82.99 % 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: 0.41 (0.28), residues: 875 helix: 1.48 (0.23), residues: 509 sheet: -0.78 (0.90), residues: 33 loop : -1.56 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 72 TYR 0.017 0.001 TYR K 40 PHE 0.014 0.001 PHE A 54 TRP 0.006 0.001 TRP K 11 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (13074) covalent geometry : angle 0.60332 / 0.36 (18784) hydrogen bonds : bond 0.05862 / 3.90 ( 690) hydrogen bonds : angle 3.87679 / 2.83 ( 1753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8354 (ptt90) cc_final: 0.7974 (ptt90) REVERT: B 27 GLN cc_start: 0.8070 (pm20) cc_final: 0.7560 (pm20) REVERT: B 98 TYR cc_start: 0.8583 (m-10) cc_final: 0.8233 (m-10) REVERT: C 82 ARG cc_start: 0.8609 (tpt90) cc_final: 0.7874 (tpt90) REVERT: C 90 ASN cc_start: 0.9071 (m110) cc_final: 0.8729 (m110) REVERT: D 71 ASP cc_start: 0.8770 (t70) cc_final: 0.8262 (t0) REVERT: F 52 GLU cc_start: 0.7716 (tp30) cc_final: 0.7502 (mm-30) REVERT: G 37 ARG cc_start: 0.7827 (mmp80) cc_final: 0.6933 (mtm-85) REVERT: G 57 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7652 (tm-30) REVERT: G 65 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7506 (tm-30) REVERT: H 71 ASP cc_start: 0.8514 (t70) cc_final: 0.7692 (t0) REVERT: H 79 GLU cc_start: 0.8450 (tp30) cc_final: 0.8000 (tp30) REVERT: K 13 ILE cc_start: 0.4921 (mt) cc_final: 0.4696 (pt) REVERT: K 52 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.6665 (ttp-170) REVERT: K 75 ARG cc_start: 0.7239 (ttp-170) cc_final: 0.6634 (mtm180) outliers start: 20 outliers final: 13 residues processed: 192 average time/residue: 0.1453 time to fit residues: 37.7385 Evaluate side-chains 173 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 50.0000 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 93 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.129786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089590 restraints weight = 33847.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.092217 restraints weight = 16826.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093856 restraints weight = 11454.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.094776 restraints weight = 9349.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095121 restraints weight = 8434.456| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 13074 Z= 0.253 Angle : 0.757 10.078 18784 Z= 0.425 Chirality : 0.049 0.392 2164 Planarity : 0.007 0.097 1475 Dihedral : 30.965 153.909 3811 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.92 % Allowed : 17.29 % Favored : 75.80 % 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: -0.58 (0.27), residues: 875 helix: 0.43 (0.21), residues: 538 sheet: -0.83 (0.89), residues: 33 loop : -1.76 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 148 TYR 0.030 0.003 TYR H 40 PHE 0.019 0.003 PHE D 73 TRP 0.002 0.001 TRP K 11 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (13074) covalent geometry : angle 0.75743 / 0.43 (18784) hydrogen bonds : bond 0.06579 / 4.33 ( 690) hydrogen bonds : angle 4.01311 / 2.92 ( 1753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8571 (ptt90) cc_final: 0.8338 (ptt-90) REVERT: A 50 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 27 GLN cc_start: 0.8426 (pm20) cc_final: 0.7925 (pm20) REVERT: B 77 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8518 (mmtm) REVERT: C 57 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 82 ARG cc_start: 0.8728 (tpt90) cc_final: 0.8031 (tpt90) REVERT: C 90 ASN cc_start: 0.9119 (m110) cc_final: 0.8817 (m-40) REVERT: C 92 ASP cc_start: 0.9075 (p0) cc_final: 0.8802 (p0) REVERT: C 93 GLU cc_start: 0.8089 (pm20) cc_final: 0.7653 (pm20) REVERT: D 46 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8526 (mttt) REVERT: D 71 ASP cc_start: 0.8853 (t70) cc_final: 0.8266 (t0) REVERT: D 79 GLU cc_start: 0.8417 (tp30) cc_final: 0.7559 (tp30) REVERT: D 116 GLU cc_start: 0.8255 (tp30) cc_final: 0.7452 (tm-30) REVERT: E 120 GLN cc_start: 0.8856 (mt0) cc_final: 0.8499 (mt0) REVERT: F 52 GLU cc_start: 0.8120 (tp30) cc_final: 0.7671 (tp30) REVERT: G 37 ARG cc_start: 0.8130 (mmp80) cc_final: 0.7123 (mtm-85) REVERT: G 57 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7503 (tm-30) REVERT: G 65 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 91 ASP cc_start: 0.7376 (t0) cc_final: 0.7062 (t0) REVERT: H 79 GLU cc_start: 0.8580 (tp30) cc_final: 0.8188 (tp30) REVERT: K 52 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.6814 (ttp-170) REVERT: K 75 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.7029 (ttm170) outliers start: 50 outliers final: 35 residues processed: 237 average time/residue: 0.1401 time to fit residues: 45.4545 Evaluate side-chains 207 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 0.0000 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 28 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.127868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.087873 restraints weight = 35754.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.090781 restraints weight = 17322.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.092623 restraints weight = 11678.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093686 restraints weight = 9473.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094158 restraints weight = 8520.532| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13074 Z= 0.168 Angle : 0.623 8.220 18784 Z= 0.363 Chirality : 0.044 0.252 2164 Planarity : 0.005 0.044 1475 Dihedral : 30.967 153.571 3811 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.84 % Allowed : 22.41 % Favored : 72.75 % 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: -0.03 (0.27), residues: 875 helix: 1.04 (0.22), residues: 528 sheet: -0.82 (0.86), residues: 33 loop : -1.79 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 83 TYR 0.025 0.002 TYR D 86 PHE 0.025 0.002 PHE F 100 TRP 0.005 0.001 TRP K 11 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (13074) covalent geometry : angle 0.62253 / 0.36 (18784) hydrogen bonds : bond 0.05193 / 3.43 ( 690) hydrogen bonds : angle 3.67624 / 2.65 ( 1753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 59 GLU cc_start: 0.8052 (pm20) cc_final: 0.7822 (pm20) REVERT: B 27 GLN cc_start: 0.8380 (pm20) cc_final: 0.7922 (pm20) REVERT: B 39 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7763 (mmm-85) REVERT: B 52 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 57 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 82 ARG cc_start: 0.8707 (tpt90) cc_final: 0.8095 (tpt90) REVERT: C 90 ASN cc_start: 0.9163 (m110) cc_final: 0.8822 (m-40) REVERT: C 93 GLU cc_start: 0.8039 (pm20) cc_final: 0.7697 (pm20) REVERT: D 46 LYS cc_start: 0.8922 (mtpp) cc_final: 0.8705 (mtmt) REVERT: D 62 MET cc_start: 0.9026 (tpt) cc_final: 0.8638 (tpp) REVERT: D 71 ASP cc_start: 0.8807 (t70) cc_final: 0.8218 (t0) REVERT: D 79 GLU cc_start: 0.8464 (tp30) cc_final: 0.7764 (tp30) REVERT: E 94 GLU cc_start: 0.8361 (tp30) cc_final: 0.8005 (tp30) REVERT: F 52 GLU cc_start: 0.8023 (tp30) cc_final: 0.7607 (tp30) REVERT: G 37 ARG cc_start: 0.8095 (mmp80) cc_final: 0.7886 (mmt90) REVERT: G 40 TYR cc_start: 0.7512 (m-80) cc_final: 0.7279 (m-10) REVERT: G 57 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7327 (tm-30) REVERT: G 65 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 93 GLU cc_start: 0.6983 (pm20) cc_final: 0.6744 (pm20) REVERT: H 79 GLU cc_start: 0.8558 (tp30) cc_final: 0.8168 (tp30) REVERT: K 52 ARG cc_start: 0.7445 (ttp-170) cc_final: 0.6724 (ttp-170) REVERT: K 75 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.7068 (ttm170) REVERT: K 92 ARG cc_start: 0.7014 (mmt180) cc_final: 0.6721 (mmt180) REVERT: K 205 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8163 (pm20) outliers start: 35 outliers final: 27 residues processed: 217 average time/residue: 0.1435 time to fit residues: 42.3302 Evaluate side-chains 208 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 6 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 205 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 = 0.4299 r_free = 0.4299 target = 0.124466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.084351 restraints weight = 35536.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.087082 restraints weight = 17269.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.088743 restraints weight = 11725.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.089790 restraints weight = 9624.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090268 restraints weight = 8685.850| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13074 Z= 0.215 Angle : 0.667 9.462 18784 Z= 0.382 Chirality : 0.045 0.245 2164 Planarity : 0.005 0.054 1475 Dihedral : 31.039 154.591 3811 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.39 % Allowed : 24.90 % Favored : 69.71 % 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: -0.08 (0.27), residues: 875 helix: 1.03 (0.22), residues: 534 sheet: -1.25 (0.79), residues: 33 loop : -1.88 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 43 TYR 0.033 0.003 TYR H 86 PHE 0.035 0.002 PHE F 100 TRP 0.011 0.002 TRP K 11 HIS 0.014 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (13074) covalent geometry : angle 0.66669 / 0.38 (18784) hydrogen bonds : bond 0.05632 / 3.74 ( 690) hydrogen bonds : angle 3.76055 / 2.71 ( 1753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8326 (tm-30) REVERT: A 59 GLU cc_start: 0.8126 (pm20) cc_final: 0.7896 (pm20) REVERT: B 27 GLN cc_start: 0.8525 (pm20) cc_final: 0.8074 (pm20) REVERT: B 52 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 57 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8093 (tm-30) REVERT: C 82 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8007 (tpt90) REVERT: C 90 ASN cc_start: 0.9138 (m110) cc_final: 0.8823 (m-40) REVERT: C 93 GLU cc_start: 0.8027 (pm20) cc_final: 0.7494 (pm20) REVERT: D 62 MET cc_start: 0.9042 (tpt) cc_final: 0.8668 (tpp) REVERT: D 71 ASP cc_start: 0.8840 (t70) cc_final: 0.8227 (t0) REVERT: D 79 GLU cc_start: 0.8467 (tp30) cc_final: 0.7800 (tp30) REVERT: D 116 GLU cc_start: 0.8165 (tp30) cc_final: 0.7368 (tm-30) REVERT: F 52 GLU cc_start: 0.8086 (tp30) cc_final: 0.7672 (tp30) REVERT: G 37 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7950 (mmt90) REVERT: G 57 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7493 (tm-30) REVERT: G 65 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7413 (tm-30) REVERT: H 79 GLU cc_start: 0.8595 (tp30) cc_final: 0.8236 (tp30) REVERT: K 52 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.6780 (ttp-170) REVERT: K 75 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.7032 (ttm170) REVERT: K 92 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6812 (mmt180) outliers start: 39 outliers final: 29 residues processed: 220 average time/residue: 0.1392 time to fit residues: 41.8876 Evaluate side-chains 211 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 40.0000 chunk 79 optimal weight: 40.0000 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.125676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085624 restraints weight = 35250.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.088431 restraints weight = 16956.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090245 restraints weight = 11438.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.091245 restraints weight = 9293.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.091777 restraints weight = 8387.418| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13074 Z= 0.160 Angle : 0.625 7.020 18784 Z= 0.364 Chirality : 0.043 0.247 2164 Planarity : 0.005 0.054 1475 Dihedral : 31.038 153.979 3811 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.70 % Allowed : 25.86 % Favored : 69.43 % 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: 0.06 (0.28), residues: 875 helix: 1.21 (0.22), residues: 532 sheet: -1.23 (0.78), residues: 33 loop : -1.94 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 148 TYR 0.031 0.003 TYR B 88 PHE 0.022 0.002 PHE F 100 TRP 0.006 0.001 TRP K 11 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (13074) covalent geometry : angle 0.62476 / 0.36 (18784) hydrogen bonds : bond 0.05129 / 3.42 ( 690) hydrogen bonds : angle 3.66054 / 2.63 ( 1753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 59 GLU cc_start: 0.8282 (pm20) cc_final: 0.7948 (pm20) REVERT: B 27 GLN cc_start: 0.8467 (pm20) cc_final: 0.8004 (pm20) REVERT: B 39 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7772 (mmm-85) REVERT: B 52 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7322 (tm-30) REVERT: C 57 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 82 ARG cc_start: 0.8738 (tpt90) cc_final: 0.7893 (tpt90) REVERT: C 90 ASN cc_start: 0.9156 (m110) cc_final: 0.8818 (m110) REVERT: C 93 GLU cc_start: 0.7977 (pm20) cc_final: 0.7482 (pm20) REVERT: D 62 MET cc_start: 0.9014 (tpt) cc_final: 0.8696 (tpp) REVERT: D 71 ASP cc_start: 0.8752 (t70) cc_final: 0.8162 (t0) REVERT: D 79 GLU cc_start: 0.8487 (tp30) cc_final: 0.7793 (tp30) REVERT: D 116 GLU cc_start: 0.8196 (tp30) cc_final: 0.7377 (tm-30) REVERT: E 94 GLU cc_start: 0.8364 (tp30) cc_final: 0.8012 (tp30) REVERT: E 95 SER cc_start: 0.8804 (t) cc_final: 0.8420 (p) REVERT: F 35 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8284 (ttp-110) REVERT: F 52 GLU cc_start: 0.7961 (tp30) cc_final: 0.7552 (tp30) REVERT: G 37 ARG cc_start: 0.8144 (mmp80) cc_final: 0.7902 (mmt90) REVERT: G 57 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7376 (tm-30) REVERT: G 65 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7416 (tm-30) REVERT: H 79 GLU cc_start: 0.8591 (tp30) cc_final: 0.8257 (tp30) REVERT: K 52 ARG cc_start: 0.7428 (ttp-170) cc_final: 0.6725 (ttp-170) REVERT: K 75 ARG cc_start: 0.7314 (ttp-170) cc_final: 0.7072 (ttm170) outliers start: 34 outliers final: 24 residues processed: 215 average time/residue: 0.1397 time to fit residues: 40.9928 Evaluate side-chains 210 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 205 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 = 0.4385 r_free = 0.4385 target = 0.127187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.087415 restraints weight = 33029.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.089941 restraints weight = 16283.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091526 restraints weight = 11060.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092345 restraints weight = 9021.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.092856 restraints weight = 8191.547| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13074 Z= 0.176 Angle : 0.647 8.124 18784 Z= 0.370 Chirality : 0.044 0.245 2164 Planarity : 0.005 0.064 1475 Dihedral : 31.049 153.884 3811 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.22 % Allowed : 25.31 % Favored : 68.46 % 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: 0.08 (0.27), residues: 875 helix: 1.20 (0.22), residues: 534 sheet: -1.39 (0.78), residues: 34 loop : -1.88 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 128 TYR 0.058 0.003 TYR B 88 PHE 0.025 0.002 PHE K 144 TRP 0.004 0.001 TRP K 11 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (13074) covalent geometry : angle 0.64671 / 0.37 (18784) hydrogen bonds : bond 0.05264 / 3.52 ( 690) hydrogen bonds : angle 3.70582 / 2.67 ( 1753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 59 GLU cc_start: 0.8341 (pm20) cc_final: 0.7986 (pm20) REVERT: B 27 GLN cc_start: 0.8434 (pm20) cc_final: 0.8169 (pm20) REVERT: B 39 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7938 (mmm-85) REVERT: B 52 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 57 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 82 ARG cc_start: 0.8747 (tpt90) cc_final: 0.7887 (tpt90) REVERT: C 90 ASN cc_start: 0.9156 (m110) cc_final: 0.8829 (m110) REVERT: C 93 GLU cc_start: 0.7967 (pm20) cc_final: 0.7430 (pm20) REVERT: D 71 ASP cc_start: 0.8675 (t70) cc_final: 0.8108 (t0) REVERT: D 116 GLU cc_start: 0.8203 (tp30) cc_final: 0.7381 (tm-30) REVERT: E 95 SER cc_start: 0.8829 (t) cc_final: 0.8501 (p) REVERT: F 52 GLU cc_start: 0.7967 (tp30) cc_final: 0.7541 (tp30) REVERT: G 57 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7486 (tm-30) REVERT: G 65 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7419 (tm-30) REVERT: K 52 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.6794 (ttp-170) REVERT: K 75 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.7148 (ttm170) outliers start: 45 outliers final: 34 residues processed: 226 average time/residue: 0.1434 time to fit residues: 44.2086 Evaluate side-chains 223 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 50.0000 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.087276 restraints weight = 33182.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.089925 restraints weight = 15817.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.091590 restraints weight = 10575.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.092531 restraints weight = 8564.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.092983 restraints weight = 7713.427| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13074 Z= 0.147 Angle : 0.634 7.321 18784 Z= 0.365 Chirality : 0.043 0.256 2164 Planarity : 0.005 0.053 1475 Dihedral : 31.033 153.078 3811 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.01 % Allowed : 28.63 % Favored : 67.36 % 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: 0.17 (0.28), residues: 875 helix: 1.31 (0.22), residues: 534 sheet: -1.40 (0.80), residues: 34 loop : -1.90 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 36 TYR 0.072 0.003 TYR B 88 PHE 0.011 0.002 PHE K 144 TRP 0.004 0.001 TRP K 11 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (13074) covalent geometry : angle 0.63389 / 0.36 (18784) hydrogen bonds : bond 0.05008 / 3.37 ( 690) hydrogen bonds : angle 3.66342 / 2.63 ( 1753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 59 GLU cc_start: 0.8270 (pm20) cc_final: 0.7943 (pm20) REVERT: B 27 GLN cc_start: 0.8435 (pm20) cc_final: 0.7980 (pm20) REVERT: B 39 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7974 (mmm-85) REVERT: B 52 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 77 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8437 (mmtt) REVERT: C 57 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8067 (tm-30) REVERT: C 82 ARG cc_start: 0.8745 (tpt90) cc_final: 0.7901 (tpt90) REVERT: C 90 ASN cc_start: 0.9157 (m110) cc_final: 0.8889 (m-40) REVERT: C 93 GLU cc_start: 0.7944 (pm20) cc_final: 0.7424 (pm20) REVERT: D 71 ASP cc_start: 0.8727 (t70) cc_final: 0.8125 (t0) REVERT: D 95 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.6871 (ttm170) REVERT: D 116 GLU cc_start: 0.8170 (tp30) cc_final: 0.7374 (tm-30) REVERT: E 94 GLU cc_start: 0.8353 (tp30) cc_final: 0.8038 (tp30) REVERT: E 95 SER cc_start: 0.8762 (t) cc_final: 0.8454 (p) REVERT: F 52 GLU cc_start: 0.7820 (tp30) cc_final: 0.7391 (tp30) REVERT: F 74 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8472 (mm-30) REVERT: G 57 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7390 (tm-30) REVERT: G 65 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7441 (tm-30) REVERT: K 52 ARG cc_start: 0.7457 (ttp-170) cc_final: 0.6783 (ttp-170) REVERT: K 75 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.7167 (ttm170) REVERT: K 92 ARG cc_start: 0.7029 (mtt180) cc_final: 0.6801 (mmt180) outliers start: 29 outliers final: 24 residues processed: 217 average time/residue: 0.1468 time to fit residues: 42.9835 Evaluate side-chains 217 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.126427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.085540 restraints weight = 33559.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.088165 restraints weight = 16312.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089852 restraints weight = 11087.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.090783 restraints weight = 9071.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091210 restraints weight = 8212.235| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13074 Z= 0.156 Angle : 0.655 11.592 18784 Z= 0.376 Chirality : 0.044 0.256 2164 Planarity : 0.005 0.056 1475 Dihedral : 31.040 152.896 3811 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.87 % Allowed : 29.46 % Favored : 66.67 % 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: 0.18 (0.28), residues: 875 helix: 1.31 (0.22), residues: 534 sheet: -1.26 (0.82), residues: 34 loop : -1.90 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 36 TYR 0.070 0.003 TYR B 88 PHE 0.016 0.001 PHE K 144 TRP 0.004 0.001 TRP K 11 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (13074) covalent geometry : angle 0.65539 / 0.38 (18784) hydrogen bonds : bond 0.05081 / 3.42 ( 690) hydrogen bonds : angle 3.70209 / 2.64 ( 1753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.7127 (p) cc_final: 0.6203 (p) REVERT: A 50 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 59 GLU cc_start: 0.8259 (pm20) cc_final: 0.7724 (pm20) REVERT: B 27 GLN cc_start: 0.8455 (pm20) cc_final: 0.8188 (pm20) REVERT: B 39 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8072 (mmm-85) REVERT: B 52 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 77 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8417 (mmtt) REVERT: C 57 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 82 ARG cc_start: 0.8755 (tpt90) cc_final: 0.7936 (tpt90) REVERT: C 90 ASN cc_start: 0.9150 (m110) cc_final: 0.8852 (m110) REVERT: C 93 GLU cc_start: 0.7945 (pm20) cc_final: 0.7429 (pm20) REVERT: D 71 ASP cc_start: 0.8749 (t70) cc_final: 0.8131 (t0) REVERT: D 95 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6890 (ttm170) REVERT: D 116 GLU cc_start: 0.8152 (tp30) cc_final: 0.7381 (tm-30) REVERT: E 95 SER cc_start: 0.8778 (t) cc_final: 0.8489 (p) REVERT: F 52 GLU cc_start: 0.7729 (tp30) cc_final: 0.7303 (tp30) REVERT: G 57 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7436 (tm-30) REVERT: G 65 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7454 (tm-30) REVERT: H 36 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6443 (mmp80) REVERT: K 43 ARG cc_start: 0.7182 (mtt90) cc_final: 0.6836 (mpt180) REVERT: K 52 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.6777 (ttp-170) REVERT: K 75 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.7197 (ttm170) outliers start: 28 outliers final: 24 residues processed: 211 average time/residue: 0.1427 time to fit residues: 40.7379 Evaluate side-chains 216 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 95 optimal weight: 50.0000 chunk 90 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.127993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.087046 restraints weight = 34802.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089506 restraints weight = 17186.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.091055 restraints weight = 11716.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.091852 restraints weight = 9584.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.092393 restraints weight = 8689.853| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13074 Z= 0.208 Angle : 0.701 10.103 18784 Z= 0.396 Chirality : 0.045 0.256 2164 Planarity : 0.006 0.070 1475 Dihedral : 31.207 153.493 3811 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.84 % Allowed : 29.18 % Favored : 65.98 % 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: 0.01 (0.27), residues: 875 helix: 1.12 (0.22), residues: 534 sheet: -0.86 (0.87), residues: 34 loop : -1.92 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 52 TYR 0.062 0.003 TYR B 88 PHE 0.013 0.002 PHE D 73 TRP 0.005 0.001 TRP K 93 HIS 0.019 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (13074) covalent geometry : angle 0.70108 / 0.40 (18784) hydrogen bonds : bond 0.05494 / 3.69 ( 690) hydrogen bonds : angle 3.86063 / 2.77 ( 1753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 59 GLU cc_start: 0.8218 (pm20) cc_final: 0.7928 (pm20) REVERT: B 27 GLN cc_start: 0.8484 (pm20) cc_final: 0.8062 (pm20) REVERT: B 39 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8154 (mmt-90) REVERT: B 52 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 57 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 82 ARG cc_start: 0.8835 (tpt90) cc_final: 0.7967 (tpt90) REVERT: C 90 ASN cc_start: 0.9125 (m110) cc_final: 0.8829 (m110) REVERT: C 93 GLU cc_start: 0.7975 (pm20) cc_final: 0.7395 (pm20) REVERT: D 71 ASP cc_start: 0.8734 (t70) cc_final: 0.8163 (t0) REVERT: D 116 GLU cc_start: 0.8225 (tp30) cc_final: 0.7457 (tm-30) REVERT: E 95 SER cc_start: 0.8775 (t) cc_final: 0.8486 (p) REVERT: F 52 GLU cc_start: 0.7857 (tp30) cc_final: 0.7402 (tp30) REVERT: F 74 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8497 (mm-30) REVERT: G 57 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7541 (tm-30) REVERT: G 65 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7443 (tm-30) REVERT: H 36 ARG cc_start: 0.7066 (mmm160) cc_final: 0.6698 (mmp80) REVERT: H 123 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8219 (tttp) REVERT: K 43 ARG cc_start: 0.7393 (mtt90) cc_final: 0.7023 (mpt180) REVERT: K 52 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.6897 (ttp-170) REVERT: K 75 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.7221 (ttm170) outliers start: 35 outliers final: 30 residues processed: 220 average time/residue: 0.1506 time to fit residues: 44.4851 Evaluate side-chains 224 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 123 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 108 optimal weight: 50.0000 chunk 40 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.124977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.084421 restraints weight = 33293.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.086956 restraints weight = 16006.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.088571 restraints weight = 10846.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.089480 restraints weight = 8852.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.089916 restraints weight = 7997.959| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13074 Z= 0.171 Angle : 0.686 10.376 18784 Z= 0.390 Chirality : 0.045 0.261 2164 Planarity : 0.005 0.066 1475 Dihedral : 31.232 153.092 3811 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.98 % Allowed : 30.15 % Favored : 64.87 % 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: 0.08 (0.28), residues: 875 helix: 1.22 (0.22), residues: 534 sheet: -0.85 (0.87), residues: 34 loop : -1.99 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 37 TYR 0.082 0.003 TYR B 88 PHE 0.035 0.002 PHE F 100 TRP 0.004 0.001 TRP K 11 HIS 0.015 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (13074) covalent geometry : angle 0.68634 / 0.39 (18784) hydrogen bonds : bond 0.05145 / 3.47 ( 690) hydrogen bonds : angle 3.80648 / 2.72 ( 1753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.04 seconds wall clock time: 49 minutes 39.40 seconds (2979.40 seconds total)