Starting phenix.real_space_refine on Thu Mar 5 09:25:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e9c_31029/03_2026/7e9c_31029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e9c_31029/03_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_31029/03_2026/7e9c_31029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e9c_31029/03_2026/7e9c_31029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e9c_31029/03_2026/7e9c_31029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e9c_31029/03_2026/7e9c_31029.map" } 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-dev-5986/lib/python3.9/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: 3.05, per 1000 atoms: 0.25 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 399.9 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: 2.03 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: 2.23 Time building geometry restraints manager: 1.38 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=" N AYA K 2 " pdb=" CT AYA K 2 " ideal model delta sigma weight residual 1.340 1.387 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" N AYA K 2 " pdb=" CA AYA K 2 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.90e-02 2.77e+03 1.23e+00 bond pdb=" CA ILE C 80 " pdb=" CB ILE C 80 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.91e-01 bond pdb=" CT AYA K 2 " pdb=" OT AYA K 2 " ideal model delta sigma weight residual 1.226 1.246 -0.020 2.00e-02 2.50e+03 9.76e-01 ... (remaining 13069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 18314 1.64 - 3.29: 411 3.29 - 4.93: 45 4.93 - 6.57: 12 6.57 - 8.22: 2 Bond angle restraints: 18784 Sorted by residual: angle pdb=" C ALA K 204 " pdb=" N GLN K 205 " pdb=" CA GLN K 205 " ideal model delta sigma weight residual 120.31 114.85 5.46 1.52e+00 4.33e-01 1.29e+01 angle pdb=" CB ARG A 52 " pdb=" CG ARG A 52 " pdb=" CD ARG A 52 " ideal model delta sigma weight residual 111.30 119.52 -8.22 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N GLN K 205 " pdb=" CA GLN K 205 " pdb=" CB GLN K 205 " ideal model delta sigma weight residual 110.28 115.34 -5.06 1.55e+00 4.16e-01 1.06e+01 angle pdb=" CB ARG A 53 " pdb=" CG ARG A 53 " pdb=" CD ARG A 53 " ideal model delta sigma weight residual 111.30 118.79 -7.49 2.30e+00 1.89e-01 1.06e+01 angle pdb=" N GLU K 206 " pdb=" CA GLU K 206 " pdb=" CB GLU K 206 " ideal model delta sigma weight residual 110.12 114.67 -4.55 1.47e+00 4.63e-01 9.56e+00 ... (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: 1878 0.047 - 0.094: 223 0.094 - 0.141: 59 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13074 Z= 0.148 Angle : 0.583 8.215 18784 Z= 0.349 Chirality : 0.035 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 covalent geometry : bond 0.00298 (13074) covalent geometry : angle 0.58284 (18784) hydrogen bonds : bond 0.11540 ( 690) hydrogen bonds : angle 4.89669 ( 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 : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7910 (pm20) cc_final: 0.7512 (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: 0.1439 time to fit residues: 39.3693 Evaluate side-chains 160 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 93 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.133743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.095128 restraints weight = 36517.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.098302 restraints weight = 17268.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.100338 restraints weight = 11405.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.101495 restraints weight = 9154.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.102075 restraints weight = 8197.145| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1947 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 : 0.575 6.540 18784 Z= 0.334 Chirality : 0.036 0.164 2164 Planarity : 0.005 0.049 1475 Dihedral : 30.488 148.611 3811 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.73 % Allowed : 14.52 % Favored : 81.74 % 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: 0.31 (0.28), residues: 875 helix: 1.36 (0.23), residues: 519 sheet: -0.68 (0.89), residues: 33 loop : -1.64 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 119 TYR 0.022 0.002 TYR D 45 PHE 0.010 0.001 PHE F 100 TRP 0.003 0.001 TRP K 11 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (13074) covalent geometry : angle 0.57512 (18784) hydrogen bonds : bond 0.04933 ( 690) hydrogen bonds : angle 3.59947 ( 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 221 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8251 (pm20) cc_final: 0.7772 (pm20) REVERT: C 34 LEU cc_start: 0.9000 (tp) cc_final: 0.8701 (tp) REVERT: C 57 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 82 ARG cc_start: 0.8637 (tpt90) cc_final: 0.7818 (tpt90) REVERT: C 90 ASN cc_start: 0.9231 (m-40) cc_final: 0.8807 (m-40) REVERT: C 93 GLU cc_start: 0.7838 (pm20) cc_final: 0.7561 (pm20) REVERT: D 46 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8557 (mtmt) REVERT: D 71 ASP cc_start: 0.8732 (t70) cc_final: 0.8132 (t0) REVERT: E 83 ARG cc_start: 0.6868 (tpt170) cc_final: 0.6619 (tpt170) REVERT: E 94 GLU cc_start: 0.8338 (tp30) cc_final: 0.8053 (tp30) REVERT: F 52 GLU cc_start: 0.7764 (tp30) cc_final: 0.7321 (tp30) REVERT: G 37 ARG cc_start: 0.7822 (mmp80) cc_final: 0.6767 (mtm-85) REVERT: G 57 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7674 (tm-30) REVERT: G 65 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7341 (tm-30) REVERT: H 40 TYR cc_start: 0.8113 (m-80) cc_final: 0.7819 (m-80) REVERT: H 62 MET cc_start: 0.8920 (tpp) cc_final: 0.8629 (tpp) REVERT: H 79 GLU cc_start: 0.8468 (tp30) cc_final: 0.8064 (tp30) REVERT: K 52 ARG cc_start: 0.7321 (ttp-170) cc_final: 0.6732 (ttp-170) REVERT: K 54 ASP cc_start: 0.6991 (m-30) cc_final: 0.6707 (p0) REVERT: K 75 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.7020 (ttm170) outliers start: 27 outliers final: 20 residues processed: 209 average time/residue: 0.1519 time to fit residues: 42.2419 Evaluate side-chains 191 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 25 THR 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 K residue 55 SER Chi-restraints excluded: chain K residue 89 THR 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: 9.9990 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 93 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.128069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087646 restraints weight = 34774.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.090656 restraints weight = 16124.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.092537 restraints weight = 10705.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.093601 restraints weight = 8693.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.094135 restraints weight = 7850.001| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13074 Z= 0.188 Angle : 0.584 6.412 18784 Z= 0.338 Chirality : 0.036 0.158 2164 Planarity : 0.005 0.049 1475 Dihedral : 30.719 148.513 3811 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.70 % Allowed : 18.81 % Favored : 76.49 % 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: 1.21 (0.22), residues: 526 sheet: -0.82 (0.85), residues: 33 loop : -1.70 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.023 0.002 TYR D 43 PHE 0.014 0.002 PHE F 100 TRP 0.003 0.001 TRP K 11 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00422 (13074) covalent geometry : angle 0.58366 (18784) hydrogen bonds : bond 0.04792 ( 690) hydrogen bonds : angle 3.62576 ( 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 250 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.7116 (p) cc_final: 0.6452 (p) REVERT: A 50 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 97 GLU cc_start: 0.8060 (tp30) cc_final: 0.7844 (mm-30) REVERT: B 27 GLN cc_start: 0.8380 (pm20) cc_final: 0.7858 (pm20) REVERT: B 39 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7789 (mmm-85) REVERT: B 52 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 77 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8400 (mmtm) REVERT: C 33 ARG cc_start: 0.8386 (ptm-80) cc_final: 0.8124 (ptm-80) REVERT: C 34 LEU cc_start: 0.9045 (tp) cc_final: 0.8782 (tp) REVERT: C 57 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 82 ARG cc_start: 0.8705 (tpt90) cc_final: 0.7912 (tpt90) REVERT: C 90 ASN cc_start: 0.9277 (m-40) cc_final: 0.8854 (m110) REVERT: C 93 GLU cc_start: 0.8032 (pm20) cc_final: 0.7571 (pm20) REVERT: D 62 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8658 (tpp) REVERT: D 71 ASP cc_start: 0.8770 (t70) cc_final: 0.8164 (t0) REVERT: D 116 GLU cc_start: 0.8013 (tp30) cc_final: 0.7192 (tm-30) REVERT: E 94 GLU cc_start: 0.8272 (tp30) cc_final: 0.7957 (tp30) REVERT: E 95 SER cc_start: 0.8843 (t) cc_final: 0.8496 (p) REVERT: F 52 GLU cc_start: 0.7949 (tp30) cc_final: 0.7526 (tp30) REVERT: G 37 ARG cc_start: 0.8106 (mmp80) cc_final: 0.7880 (mmt90) REVERT: G 40 TYR cc_start: 0.7645 (m-10) cc_final: 0.7347 (m-80) REVERT: G 57 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7592 (tm-30) REVERT: G 65 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7391 (tm-30) REVERT: H 36 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7056 (mmm160) REVERT: H 62 MET cc_start: 0.8905 (tpp) cc_final: 0.8590 (tpp) REVERT: H 79 GLU cc_start: 0.8545 (tp30) cc_final: 0.8220 (tp30) REVERT: H 122 THR cc_start: 0.9076 (m) cc_final: 0.8869 (p) REVERT: K 52 ARG cc_start: 0.7438 (ttp-170) cc_final: 0.6943 (ttp-170) REVERT: K 75 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.7030 (ttm170) REVERT: K 142 GLN cc_start: 0.8873 (tt0) cc_final: 0.8539 (tt0) outliers start: 34 outliers final: 23 residues processed: 232 average time/residue: 0.1623 time to fit residues: 48.9928 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 : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 C residue 53 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU 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 Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** E 93 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 77 ASN ** 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 = 0.4307 r_free = 0.4307 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082054 restraints weight = 33290.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.084489 restraints weight = 16248.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.086010 restraints weight = 11159.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.086851 restraints weight = 9212.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.087166 restraints weight = 8399.411| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13074 Z= 0.232 Angle : 0.634 8.912 18784 Z= 0.365 Chirality : 0.039 0.194 2164 Planarity : 0.006 0.093 1475 Dihedral : 31.170 148.242 3811 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.64 % Allowed : 21.72 % Favored : 71.65 % 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 (0.27), residues: 875 helix: 0.94 (0.22), residues: 536 sheet: -0.61 (0.92), residues: 29 loop : -1.98 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 83 TYR 0.024 0.002 TYR D 86 PHE 0.031 0.002 PHE F 100 TRP 0.006 0.002 TRP K 11 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00532 (13074) covalent geometry : angle 0.63383 (18784) hydrogen bonds : bond 0.05232 ( 690) hydrogen bonds : angle 3.77390 ( 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 261 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 52 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8345 (mtm-85) REVERT: A 97 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: B 27 GLN cc_start: 0.8556 (pm20) cc_final: 0.8154 (pm20) REVERT: B 52 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 77 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8761 (mmtt) REVERT: B 88 TYR cc_start: 0.8587 (m-10) cc_final: 0.8312 (m-10) REVERT: C 57 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 82 ARG cc_start: 0.8852 (tpt90) cc_final: 0.8139 (tpt90) REVERT: D 102 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8263 (ptp-110) REVERT: D 116 GLU cc_start: 0.8102 (tp30) cc_final: 0.7404 (tm-30) REVERT: E 95 SER cc_start: 0.8801 (t) cc_final: 0.8518 (p) REVERT: F 52 GLU cc_start: 0.8125 (tp30) cc_final: 0.7682 (tp30) REVERT: F 77 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8896 (mmtp) REVERT: G 37 ARG cc_start: 0.8328 (mmp80) cc_final: 0.8111 (mmt90) REVERT: G 57 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7568 (tm-30) REVERT: G 65 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7452 (tm-30) REVERT: G 91 ASP cc_start: 0.7225 (t0) cc_final: 0.6861 (t0) REVERT: H 36 ARG cc_start: 0.7683 (mmm160) cc_final: 0.7226 (mmm160) REVERT: H 46 LYS cc_start: 0.8872 (mttp) cc_final: 0.8628 (mttp) REVERT: H 62 MET cc_start: 0.9024 (tpp) cc_final: 0.8614 (tpp) REVERT: H 79 GLU cc_start: 0.8524 (tp30) cc_final: 0.8322 (tp30) REVERT: H 122 THR cc_start: 0.9158 (m) cc_final: 0.8905 (p) REVERT: K 52 ARG cc_start: 0.7497 (ttp-170) cc_final: 0.7029 (ttp-170) REVERT: K 75 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.7167 (ttm170) outliers start: 48 outliers final: 35 residues processed: 237 average time/residue: 0.1453 time to fit residues: 46.1291 Evaluate side-chains 238 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 97 GLU 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 66 ILE Chi-restraints excluded: chain B residue 80 THR 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 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN ** 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.079836 restraints weight = 35556.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.082498 restraints weight = 16861.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.084229 restraints weight = 11432.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.085133 restraints weight = 9353.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085320 restraints weight = 8501.781| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13074 Z= 0.198 Angle : 0.602 7.463 18784 Z= 0.350 Chirality : 0.037 0.182 2164 Planarity : 0.005 0.058 1475 Dihedral : 31.075 147.333 3811 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.22 % Allowed : 25.17 % Favored : 68.60 % 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: 1.17 (0.22), residues: 534 sheet: -0.65 (0.91), residues: 29 loop : -2.06 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 83 TYR 0.036 0.002 TYR D 86 PHE 0.030 0.002 PHE F 100 TRP 0.007 0.001 TRP K 11 HIS 0.013 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00452 (13074) covalent geometry : angle 0.60169 (18784) hydrogen bonds : bond 0.04793 ( 690) hydrogen bonds : angle 3.65799 ( 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 263 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 52 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8318 (mtt90) REVERT: B 27 GLN cc_start: 0.8558 (pm20) cc_final: 0.8121 (pm20) REVERT: B 39 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8107 (mmt-90) REVERT: B 44 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8701 (mmmm) REVERT: B 52 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 77 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8742 (mmtt) REVERT: B 88 TYR cc_start: 0.8555 (m-10) cc_final: 0.8278 (m-10) REVERT: C 57 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 82 ARG cc_start: 0.8844 (tpt90) cc_final: 0.8007 (tpt90) REVERT: C 93 GLU cc_start: 0.8181 (pm20) cc_final: 0.7680 (pm20) REVERT: D 88 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8863 (mmtp) REVERT: D 95 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7050 (ttm170) REVERT: D 116 GLU cc_start: 0.8049 (tp30) cc_final: 0.7294 (tm-30) REVERT: E 95 SER cc_start: 0.8738 (t) cc_final: 0.8442 (p) REVERT: F 52 GLU cc_start: 0.7916 (tp30) cc_final: 0.7474 (tp30) REVERT: F 77 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8954 (mmtp) REVERT: G 57 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7668 (tm-30) REVERT: G 65 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7437 (tm-30) REVERT: G 91 ASP cc_start: 0.7239 (t0) cc_final: 0.7023 (t0) REVERT: G 93 GLU cc_start: 0.6730 (pm20) cc_final: 0.6524 (pm20) REVERT: H 62 MET cc_start: 0.8945 (tpp) cc_final: 0.8574 (tpp) REVERT: H 122 THR cc_start: 0.9175 (m) cc_final: 0.8924 (p) REVERT: K 52 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.6795 (ttp-170) REVERT: K 75 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7248 (ttm170) REVERT: K 142 GLN cc_start: 0.8781 (mt0) cc_final: 0.8471 (tt0) outliers start: 45 outliers final: 30 residues processed: 240 average time/residue: 0.1491 time to fit residues: 47.6419 Evaluate side-chains 235 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR 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 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 101 VAL 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 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU 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 176 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** E 93 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 ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4322 r_free = 0.4322 target = 0.123604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083316 restraints weight = 33512.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.085881 restraints weight = 16077.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.087490 restraints weight = 10980.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.088373 restraints weight = 9056.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.088695 restraints weight = 8254.847| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13074 Z= 0.158 Angle : 0.587 8.290 18784 Z= 0.340 Chirality : 0.036 0.201 2164 Planarity : 0.004 0.047 1475 Dihedral : 30.935 145.953 3811 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.26 % Allowed : 27.11 % Favored : 67.63 % 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: 0.20 (0.28), residues: 875 helix: 1.35 (0.22), residues: 546 sheet: -0.25 (1.01), residues: 23 loop : -2.17 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 36 TYR 0.029 0.002 TYR D 86 PHE 0.025 0.002 PHE F 100 TRP 0.009 0.002 TRP K 11 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00355 (13074) covalent geometry : angle 0.58739 (18784) hydrogen bonds : bond 0.04563 ( 690) hydrogen bonds : angle 3.51305 ( 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 249 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 52 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: B 27 GLN cc_start: 0.8618 (pm20) cc_final: 0.8148 (pm20) REVERT: B 44 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8667 (mmmm) REVERT: B 52 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 33 ARG cc_start: 0.8588 (ptm-80) cc_final: 0.8359 (ptm-80) REVERT: C 82 ARG cc_start: 0.8818 (tpt90) cc_final: 0.8066 (tpt90) REVERT: C 93 GLU cc_start: 0.8150 (pm20) cc_final: 0.7646 (pm20) REVERT: E 94 GLU cc_start: 0.8408 (tp30) cc_final: 0.8066 (tp30) REVERT: E 95 SER cc_start: 0.8665 (t) cc_final: 0.8442 (p) REVERT: F 52 GLU cc_start: 0.7694 (tp30) cc_final: 0.7241 (tp30) REVERT: F 77 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8893 (mmtp) REVERT: G 57 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7815 (tm-30) REVERT: G 65 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7439 (tm-30) REVERT: G 91 ASP cc_start: 0.7157 (t0) cc_final: 0.6932 (t0) REVERT: H 49 LYS cc_start: 0.9135 (mmtp) cc_final: 0.8913 (mmtp) REVERT: H 62 MET cc_start: 0.8945 (tpp) cc_final: 0.8593 (tpp) REVERT: H 122 THR cc_start: 0.9118 (m) cc_final: 0.8888 (p) REVERT: K 52 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6807 (ttp-170) REVERT: K 75 ARG cc_start: 0.7512 (ttp-170) cc_final: 0.7301 (ttm170) REVERT: K 142 GLN cc_start: 0.8681 (mt0) cc_final: 0.8398 (tt0) REVERT: K 206 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7218 (mp0) outliers start: 38 outliers final: 30 residues processed: 229 average time/residue: 0.1349 time to fit residues: 42.0694 Evaluate side-chains 231 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 107 THR 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 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 65 LEU 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 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 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 69 VAL Chi-restraints excluded: chain K residue 16 THR 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 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU 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: 40.0000 chunk 87 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 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 ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4209 r_free = 0.4209 target = 0.117619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.077519 restraints weight = 34909.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080129 restraints weight = 16626.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.081730 restraints weight = 11355.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.082629 restraints weight = 9383.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.082874 restraints weight = 8546.027| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13074 Z= 0.220 Angle : 0.633 8.185 18784 Z= 0.364 Chirality : 0.038 0.187 2164 Planarity : 0.005 0.064 1475 Dihedral : 31.153 147.444 3811 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.09 % Allowed : 26.83 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 875 helix: 1.13 (0.22), residues: 546 sheet: -0.67 (0.88), residues: 33 loop : -2.11 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 33 TYR 0.029 0.002 TYR D 86 PHE 0.010 0.001 PHE A 54 TRP 0.006 0.001 TRP K 86 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00506 (13074) covalent geometry : angle 0.63274 (18784) hydrogen bonds : bond 0.05120 ( 690) hydrogen bonds : angle 3.72834 ( 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 255 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 52 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.7987 (mtm180) REVERT: B 27 GLN cc_start: 0.8567 (pm20) cc_final: 0.8201 (pm20) REVERT: B 39 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8331 (mmt-90) REVERT: B 52 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 33 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8454 (ptm-80) REVERT: C 40 TYR cc_start: 0.7562 (m-80) cc_final: 0.7342 (m-80) REVERT: C 82 ARG cc_start: 0.8916 (tpt90) cc_final: 0.7998 (tpt90) REVERT: C 93 GLU cc_start: 0.8187 (pm20) cc_final: 0.7760 (pm20) REVERT: E 94 GLU cc_start: 0.8402 (tp30) cc_final: 0.7984 (tp30) REVERT: E 95 SER cc_start: 0.8694 (t) cc_final: 0.8408 (p) REVERT: F 52 GLU cc_start: 0.8048 (tp30) cc_final: 0.7599 (tp30) REVERT: F 77 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8969 (mmtp) REVERT: G 57 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7624 (tm-30) REVERT: G 65 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7494 (tm-30) REVERT: H 62 MET cc_start: 0.8988 (tpp) cc_final: 0.8573 (tpp) REVERT: K 52 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.6823 (ttp-170) REVERT: K 206 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7246 (mp0) outliers start: 44 outliers final: 32 residues processed: 234 average time/residue: 0.1440 time to fit residues: 44.9239 Evaluate side-chains 228 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR 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 65 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 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 107 THR 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 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 16 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 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 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 ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4344 r_free = 0.4344 target = 0.125092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085162 restraints weight = 33470.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.087793 restraints weight = 15520.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.089450 restraints weight = 10422.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090370 restraints weight = 8523.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.090805 restraints weight = 7723.081| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13074 Z= 0.146 Angle : 0.614 13.661 18784 Z= 0.348 Chirality : 0.036 0.168 2164 Planarity : 0.004 0.049 1475 Dihedral : 30.854 147.002 3811 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.15 % Allowed : 29.32 % Favored : 66.53 % 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: 0.26 (0.28), residues: 875 helix: 1.36 (0.22), residues: 553 sheet: -0.42 (0.90), residues: 33 loop : -2.19 (0.31), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 33 TYR 0.023 0.002 TYR D 86 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP K 11 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00321 (13074) covalent geometry : angle 0.61426 (18784) hydrogen bonds : bond 0.04518 ( 690) hydrogen bonds : angle 3.52602 ( 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 237 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8235 (tm-30) REVERT: A 52 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.7856 (ptp90) REVERT: A 63 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7146 (tpm170) REVERT: B 27 GLN cc_start: 0.8435 (pm20) cc_final: 0.7987 (pm20) REVERT: B 52 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 33 ARG cc_start: 0.8478 (ptm-80) cc_final: 0.8262 (ptm-80) REVERT: C 82 ARG cc_start: 0.8818 (tpt90) cc_final: 0.8039 (tpt90) REVERT: C 93 GLU cc_start: 0.8209 (pm20) cc_final: 0.7976 (pm20) REVERT: D 62 MET cc_start: 0.8863 (tpp) cc_final: 0.8492 (tpp) REVERT: E 94 GLU cc_start: 0.8309 (tp30) cc_final: 0.7999 (tp30) REVERT: F 52 GLU cc_start: 0.7573 (tp30) cc_final: 0.7097 (tp30) REVERT: F 74 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8662 (mm-30) REVERT: F 77 LYS cc_start: 0.9227 (mmtm) cc_final: 0.8943 (mmtp) REVERT: G 57 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7832 (tm-30) REVERT: G 65 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7423 (tm-30) REVERT: H 49 LYS cc_start: 0.9078 (mmtp) cc_final: 0.8838 (mmtp) REVERT: H 62 MET cc_start: 0.8895 (tpp) cc_final: 0.8629 (tpt) REVERT: K 52 ARG cc_start: 0.7274 (ttp-170) cc_final: 0.6739 (ttp-170) REVERT: K 142 GLN cc_start: 0.8665 (mt0) cc_final: 0.8377 (tt0) outliers start: 30 outliers final: 24 residues processed: 220 average time/residue: 0.1457 time to fit residues: 42.9369 Evaluate side-chains 219 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS 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 96 VAL 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 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 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 69 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 103 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** E 93 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 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4318 r_free = 0.4318 target = 0.123650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083594 restraints weight = 33544.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086146 restraints weight = 16073.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087745 restraints weight = 10974.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088649 restraints weight = 9052.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089057 restraints weight = 8237.494| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13074 Z= 0.157 Angle : 0.613 12.167 18784 Z= 0.349 Chirality : 0.036 0.171 2164 Planarity : 0.005 0.075 1475 Dihedral : 30.852 146.912 3811 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.29 % Allowed : 30.01 % Favored : 65.70 % 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: 0.34 (0.28), residues: 875 helix: 1.35 (0.22), residues: 555 sheet: -0.34 (0.91), residues: 33 loop : -2.00 (0.32), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 43 TYR 0.027 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.017 0.003 TRP K 11 HIS 0.013 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (13074) covalent geometry : angle 0.61301 (18784) hydrogen bonds : bond 0.04505 ( 690) hydrogen bonds : angle 3.52200 ( 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 234 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 52 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8002 (mtm180) REVERT: B 27 GLN cc_start: 0.8472 (pm20) cc_final: 0.8062 (pm20) REVERT: B 52 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 77 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8588 (mmtt) REVERT: C 33 ARG cc_start: 0.8557 (ptm-80) cc_final: 0.8276 (ptm-80) REVERT: C 65 GLU cc_start: 0.8377 (tp30) cc_final: 0.8113 (tp30) REVERT: C 82 ARG cc_start: 0.8863 (tpt90) cc_final: 0.8047 (tpt90) REVERT: C 93 GLU cc_start: 0.8187 (pm20) cc_final: 0.7836 (pm20) REVERT: D 62 MET cc_start: 0.8894 (tpp) cc_final: 0.8547 (tpp) REVERT: D 116 GLU cc_start: 0.8174 (tp30) cc_final: 0.7249 (tm-30) REVERT: E 94 GLU cc_start: 0.8388 (tp30) cc_final: 0.8010 (tp30) REVERT: F 52 GLU cc_start: 0.7612 (tp30) cc_final: 0.7140 (tp30) REVERT: F 74 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8633 (mm-30) REVERT: F 77 LYS cc_start: 0.9211 (mmtm) cc_final: 0.8876 (mmtp) REVERT: G 57 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7690 (tm-30) REVERT: G 65 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7505 (tm-30) REVERT: H 62 MET cc_start: 0.8904 (tpp) cc_final: 0.8578 (tpp) REVERT: K 52 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6699 (ttp-170) REVERT: K 142 GLN cc_start: 0.8685 (mt0) cc_final: 0.8410 (tt0) outliers start: 31 outliers final: 27 residues processed: 217 average time/residue: 0.1328 time to fit residues: 39.2438 Evaluate side-chains 221 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 39 THR 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 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 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 69 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** E 93 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 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.124303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084408 restraints weight = 33516.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.086974 restraints weight = 16013.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.088590 restraints weight = 10847.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089475 restraints weight = 8898.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089989 restraints weight = 8078.103| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13074 Z= 0.156 Angle : 0.620 12.071 18784 Z= 0.351 Chirality : 0.037 0.171 2164 Planarity : 0.005 0.069 1475 Dihedral : 30.827 146.977 3811 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.43 % Allowed : 30.71 % 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: 0.31 (0.28), residues: 875 helix: 1.32 (0.22), residues: 558 sheet: -0.35 (0.90), residues: 33 loop : -2.04 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 43 TYR 0.022 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.011 0.002 TRP K 11 HIS 0.014 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (13074) covalent geometry : angle 0.61956 (18784) hydrogen bonds : bond 0.04529 ( 690) hydrogen bonds : angle 3.53849 ( 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 225 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 52 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: B 27 GLN cc_start: 0.8457 (pm20) cc_final: 0.8019 (pm20) REVERT: B 52 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 33 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8323 (ptm-80) REVERT: C 39 ASN cc_start: 0.7653 (t0) cc_final: 0.7445 (t0) REVERT: C 59 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8028 (tt) REVERT: C 65 GLU cc_start: 0.8374 (tp30) cc_final: 0.8109 (tp30) REVERT: C 82 ARG cc_start: 0.8864 (tpt90) cc_final: 0.8040 (tpt90) REVERT: D 62 MET cc_start: 0.8881 (tpp) cc_final: 0.8560 (tpp) REVERT: D 116 GLU cc_start: 0.8168 (tp30) cc_final: 0.7156 (tm-30) REVERT: E 94 GLU cc_start: 0.8361 (tp30) cc_final: 0.7971 (tp30) REVERT: F 52 GLU cc_start: 0.7579 (tp30) cc_final: 0.7113 (tp30) REVERT: F 74 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8608 (mm-30) REVERT: F 77 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8874 (mmtp) REVERT: G 57 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7596 (tm-30) REVERT: G 65 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 62 MET cc_start: 0.8902 (tpp) cc_final: 0.8592 (tpp) REVERT: K 52 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6695 (ttp-170) REVERT: K 142 GLN cc_start: 0.8661 (mt0) cc_final: 0.8394 (tt0) outliers start: 32 outliers final: 27 residues processed: 208 average time/residue: 0.1280 time to fit residues: 36.1136 Evaluate side-chains 218 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU 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 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 34 LEU 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 69 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN ** F 25 ASN ** 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 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4225 r_free = 0.4225 target = 0.118579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079739 restraints weight = 34804.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082123 restraints weight = 17989.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083629 restraints weight = 12590.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084494 restraints weight = 10429.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.084880 restraints weight = 9495.415| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13074 Z= 0.177 Angle : 0.627 11.718 18784 Z= 0.356 Chirality : 0.037 0.176 2164 Planarity : 0.005 0.070 1475 Dihedral : 30.905 147.328 3811 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.43 % Allowed : 30.84 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.28), residues: 875 helix: 1.37 (0.22), residues: 551 sheet: -0.40 (0.89), residues: 33 loop : -2.04 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 43 TYR 0.046 0.002 TYR F 88 PHE 0.007 0.001 PHE B 100 TRP 0.010 0.002 TRP K 11 HIS 0.014 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (13074) covalent geometry : angle 0.62656 (18784) hydrogen bonds : bond 0.04673 ( 690) hydrogen bonds : angle 3.60723 ( 1753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.26 seconds wall clock time: 48 minutes 9.74 seconds (2889.74 seconds total)