Starting phenix.real_space_refine on Thu Sep 18 19:23:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kr2_23000/09_2025/7kr2_23000.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kr2_23000/09_2025/7kr2_23000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kr2_23000/09_2025/7kr2_23000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kr2_23000/09_2025/7kr2_23000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kr2_23000/09_2025/7kr2_23000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kr2_23000/09_2025/7kr2_23000.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.231 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12530 2.51 5 N 3318 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 2.28, per 1000 atoms: 0.12 Number of scatterers: 19712 At special positions: 0 Unit cell: (115.54, 113.42, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3752 8.00 N 3318 7.00 C 12530 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: 1.83 Conformation dependent library (CDL) restraints added in 936.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4732 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 42 sheets defined 48.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 41 through 59 Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'C' and resid 24 through 30 Processing helix chain 'C' and resid 41 through 59 Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.546A pdb=" N ILE C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 41 through 59 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 41 through 59 Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 175 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 41 through 59 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'G' and resid 24 through 30 Processing helix chain 'G' and resid 41 through 59 Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 182 through 190 Processing helix chain 'H' and resid 24 through 30 Processing helix chain 'H' and resid 41 through 59 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 102 through 110 Processing helix chain 'H' and resid 147 through 165 removed outlier: 3.544A pdb=" N ILE H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 175 Processing helix chain 'H' and resid 182 through 190 Processing helix chain 'I' and resid 24 through 30 Processing helix chain 'I' and resid 41 through 59 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 175 Processing helix chain 'I' and resid 182 through 190 Processing helix chain 'J' and resid 24 through 30 Processing helix chain 'J' and resid 41 through 59 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'K' and resid 24 through 30 Processing helix chain 'K' and resid 41 through 59 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE K 152 " --> pdb=" O GLU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 175 Processing helix chain 'K' and resid 182 through 190 Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 41 through 59 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 102 through 110 Processing helix chain 'L' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE L 152 " --> pdb=" O GLU L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 175 Processing helix chain 'L' and resid 182 through 190 Processing helix chain 'M' and resid 24 through 30 Processing helix chain 'M' and resid 41 through 59 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 147 through 165 removed outlier: 3.545A pdb=" N ILE M 152 " --> pdb=" O GLU M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 175 Processing helix chain 'M' and resid 182 through 190 Processing helix chain 'N' and resid 24 through 30 Processing helix chain 'N' and resid 41 through 59 Processing helix chain 'N' and resid 74 through 88 Processing helix chain 'N' and resid 102 through 110 Processing helix chain 'N' and resid 147 through 165 removed outlier: 3.544A pdb=" N ILE N 152 " --> pdb=" O GLU N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 175 Processing helix chain 'N' and resid 182 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER A 70 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN A 99 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 123 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A 98 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 125 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 100 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER A 70 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN A 99 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE A 117 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 94 " --> pdb=" O PHE A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER B 70 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 99 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG B 123 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY B 98 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET B 125 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 100 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER B 70 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 99 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE B 117 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR B 94 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER C 70 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN C 99 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 123 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY C 98 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET C 125 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 100 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER C 70 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN C 99 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE C 117 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR C 94 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER D 70 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN D 99 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG D 123 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY D 98 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET D 125 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 100 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER D 70 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN D 99 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE D 117 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR D 94 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'E' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER E 70 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN E 99 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG E 123 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY E 98 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET E 125 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA E 100 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER E 70 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN E 99 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE E 117 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR E 94 " --> pdb=" O PHE E 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER F 70 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN F 99 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG F 123 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY F 98 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET F 125 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA F 100 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER F 70 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN F 99 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE F 117 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR F 94 " --> pdb=" O PHE F 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER G 70 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN G 99 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG G 123 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY G 98 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET G 125 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA G 100 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER G 70 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN G 99 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE G 117 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR G 94 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AC5, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG H 123 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY H 98 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET H 125 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA H 100 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER H 70 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN H 99 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE H 117 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR H 94 " --> pdb=" O PHE H 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG I 123 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY I 98 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET I 125 " --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA I 100 " --> pdb=" O MET I 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER I 70 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN I 99 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE I 117 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR I 94 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD2, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG J 123 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY J 98 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET J 125 " --> pdb=" O GLY J 98 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA J 100 " --> pdb=" O MET J 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER J 70 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN J 99 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE J 117 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR J 94 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG K 123 " --> pdb=" O CYS K 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY K 98 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET K 125 " --> pdb=" O GLY K 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA K 100 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER K 70 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN K 99 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE K 117 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR K 94 " --> pdb=" O PHE K 117 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AD8, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG L 123 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY L 98 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET L 125 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA L 100 " --> pdb=" O MET L 125 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER L 70 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN L 99 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE L 117 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR L 94 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AE2, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG M 123 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY M 98 " --> pdb=" O ARG M 123 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET M 125 " --> pdb=" O GLY M 98 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA M 100 " --> pdb=" O MET M 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.193A pdb=" N SER M 70 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN M 99 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE M 117 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR M 94 " --> pdb=" O PHE M 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG N 123 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY N 98 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET N 125 " --> pdb=" O GLY N 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA N 100 " --> pdb=" O MET N 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.192A pdb=" N SER N 70 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN N 99 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE N 117 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR N 94 " --> pdb=" O PHE N 117 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4640 1.32 - 1.45: 5442 1.45 - 1.58: 9728 1.58 - 1.71: 0 1.71 - 1.85: 196 Bond restraints: 20006 Sorted by residual: bond pdb=" CB ASP N 23 " pdb=" CG ASP N 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.35e+01 bond pdb=" CB ASP J 23 " pdb=" CG ASP J 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.34e+01 bond pdb=" CB ASP G 23 " pdb=" CG ASP G 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.34e+01 bond pdb=" CB ASP C 23 " pdb=" CG ASP C 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.33e+01 bond pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.33e+01 ... (remaining 20001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 21548 1.83 - 3.65: 4237 3.65 - 5.47: 896 5.47 - 7.30: 199 7.30 - 9.12: 56 Bond angle restraints: 26936 Sorted by residual: angle pdb=" C ASN J 59 " pdb=" N PRO J 60 " pdb=" CA PRO J 60 " ideal model delta sigma weight residual 119.56 127.04 -7.48 1.02e+00 9.61e-01 5.37e+01 angle pdb=" C ASN I 59 " pdb=" N PRO I 60 " pdb=" CA PRO I 60 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.36e+01 angle pdb=" C ASN H 59 " pdb=" N PRO H 60 " pdb=" CA PRO H 60 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.35e+01 angle pdb=" C ASN F 59 " pdb=" N PRO F 60 " pdb=" CA PRO F 60 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.35e+01 angle pdb=" C ASN C 59 " pdb=" N PRO C 60 " pdb=" CA PRO C 60 " ideal model delta sigma weight residual 119.56 126.99 -7.43 1.02e+00 9.61e-01 5.31e+01 ... (remaining 26931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 11690 15.90 - 31.79: 420 31.79 - 47.69: 112 47.69 - 63.59: 84 63.59 - 79.49: 28 Dihedral angle restraints: 12334 sinusoidal: 5082 harmonic: 7252 Sorted by residual: dihedral pdb=" CA ASP N 23 " pdb=" CB ASP N 23 " pdb=" CG ASP N 23 " pdb=" OD1 ASP N 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.62 55.62 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASP C 23 " pdb=" CB ASP C 23 " pdb=" CG ASP C 23 " pdb=" OD1 ASP C 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASP I 23 " pdb=" CB ASP I 23 " pdb=" CG ASP I 23 " pdb=" OD1 ASP I 23 " ideal model delta sinusoidal sigma weight residual -30.00 -85.57 55.57 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 12331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1661 0.064 - 0.128: 1000 0.128 - 0.192: 276 0.192 - 0.256: 129 0.256 - 0.320: 14 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA LYS D 89 " pdb=" N LYS D 89 " pdb=" C LYS D 89 " pdb=" CB LYS D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA LYS B 89 " pdb=" N LYS B 89 " pdb=" C LYS B 89 " pdb=" CB LYS B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA LYS K 89 " pdb=" N LYS K 89 " pdb=" C LYS K 89 " pdb=" CB LYS K 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 3077 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 25 " -0.037 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR N 25 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR N 25 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR N 25 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR N 25 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR N 25 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR N 25 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 25 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 25 " -0.037 2.00e-02 2.50e+03 2.03e-02 8.24e+00 pdb=" CG TYR B 25 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 25 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 25 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 25 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 25 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 25 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 25 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 25 " 0.037 2.00e-02 2.50e+03 2.03e-02 8.22e+00 pdb=" CG TYR I 25 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR I 25 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR I 25 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR I 25 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR I 25 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR I 25 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 25 " 0.029 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 8201 2.91 - 3.41: 19931 3.41 - 3.91: 34285 3.91 - 4.40: 40654 4.40 - 4.90: 64907 Nonbonded interactions: 167978 Sorted by model distance: nonbonded pdb=" OD1 ASP B 61 " pdb=" NZ LYS B 89 " model vdw 2.415 3.120 nonbonded pdb=" OD1 ASP L 61 " pdb=" NZ LYS L 89 " model vdw 2.416 3.120 nonbonded pdb=" OD1 ASP J 61 " pdb=" NZ LYS J 89 " model vdw 2.416 3.120 nonbonded pdb=" OD1 ASP K 61 " pdb=" NZ LYS K 89 " model vdw 2.416 3.120 nonbonded pdb=" OD1 ASP H 61 " pdb=" NZ LYS H 89 " model vdw 2.416 3.120 ... (remaining 167973 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.690 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.020 0.121 20006 Z= 1.062 Angle : 1.650 9.125 26936 Z= 1.135 Chirality : 0.090 0.320 3080 Planarity : 0.009 0.046 3486 Dihedral : 11.595 79.487 7602 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 0.65 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.15), residues: 2408 helix: -0.59 (0.12), residues: 1246 sheet: 1.61 (0.30), residues: 308 loop : -0.95 (0.17), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 116 TYR 0.037 0.009 TYR I 25 PHE 0.026 0.008 PHE H 22 HIS 0.004 0.002 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.01967 (20006) covalent geometry : angle 1.64965 (26936) hydrogen bonds : bond 0.14887 ( 1022) hydrogen bonds : angle 7.12872 ( 3360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 919 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 VAL cc_start: 0.8262 (t) cc_final: 0.7967 (p) REVERT: F 40 VAL cc_start: 0.8056 (t) cc_final: 0.7841 (p) REVERT: F 125 MET cc_start: 0.7684 (ttm) cc_final: 0.7389 (ttp) REVERT: F 145 HIS cc_start: 0.6023 (m170) cc_final: 0.5805 (m90) REVERT: N 23 ASP cc_start: 0.6637 (p0) cc_final: 0.6302 (p0) REVERT: N 125 MET cc_start: 0.7555 (ttm) cc_final: 0.7345 (ttp) outliers start: 14 outliers final: 0 residues processed: 919 average time/residue: 0.1708 time to fit residues: 223.1595 Evaluate side-chains 413 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS B 46 ASN B 86 ASN B 128 GLN C 46 ASN D 46 ASN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 86 ASN E 128 GLN F 46 ASN F 128 GLN G 46 ASN G 86 ASN G 128 GLN H 46 ASN H 86 ASN H 128 GLN I 46 ASN J 46 ASN J 51 GLN J 128 GLN K 46 ASN K 86 ASN K 128 GLN K 157 ASN L 46 ASN L 86 ASN L 128 GLN M 86 ASN N 86 ASN N 128 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107741 restraints weight = 25948.005| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.68 r_work: 0.3305 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20006 Z= 0.149 Angle : 0.657 6.162 26936 Z= 0.342 Chirality : 0.046 0.151 3080 Planarity : 0.005 0.039 3486 Dihedral : 4.830 24.113 2660 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.17 % Allowed : 11.80 % Favored : 86.04 % 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 aren not related in a simple way. whole: 0.76 (0.16), residues: 2408 helix: 0.95 (0.15), residues: 1260 sheet: 1.14 (0.35), residues: 196 loop : -0.11 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 147 TYR 0.022 0.001 TYR I 82 PHE 0.036 0.002 PHE F 54 HIS 0.012 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00329 (20006) covalent geometry : angle 0.65737 (26936) hydrogen bonds : bond 0.04642 ( 1022) hydrogen bonds : angle 4.39737 ( 3360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 476 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 THR cc_start: 0.8518 (p) cc_final: 0.8298 (p) REVERT: A 173 ARG cc_start: 0.8500 (tmm-80) cc_final: 0.8235 (ttp80) REVERT: B 181 MET cc_start: 0.8388 (mtp) cc_final: 0.8180 (mtm) REVERT: C 173 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7626 (ptp90) REVERT: C 177 ARG cc_start: 0.7522 (ptt180) cc_final: 0.7012 (ptt90) REVERT: C 181 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: D 79 MET cc_start: 0.8805 (mmm) cc_final: 0.8278 (mmt) REVERT: E 173 ARG cc_start: 0.8406 (tmm-80) cc_final: 0.8134 (tmm-80) REVERT: E 181 MET cc_start: 0.8355 (mtp) cc_final: 0.8027 (mtm) REVERT: F 125 MET cc_start: 0.8268 (ttm) cc_final: 0.7992 (ttp) REVERT: F 166 ARG cc_start: 0.8379 (mmt90) cc_final: 0.7995 (mmm160) REVERT: F 172 GLU cc_start: 0.8638 (tt0) cc_final: 0.8067 (mt-10) REVERT: F 173 ARG cc_start: 0.8463 (ttp80) cc_final: 0.7715 (ptt-90) REVERT: G 173 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.8103 (tmm-80) REVERT: G 177 ARG cc_start: 0.7238 (mtm180) cc_final: 0.6656 (ptt90) REVERT: G 181 MET cc_start: 0.8417 (mtp) cc_final: 0.7991 (mtm) REVERT: H 113 LYS cc_start: 0.7839 (tppt) cc_final: 0.7606 (mmtm) REVERT: H 173 ARG cc_start: 0.8387 (tmm-80) cc_final: 0.8134 (ttp80) REVERT: H 177 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6809 (ptt90) REVERT: I 30 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8682 (ttmm) REVERT: I 79 MET cc_start: 0.8453 (mmm) cc_final: 0.8218 (mmm) REVERT: I 177 ARG cc_start: 0.7763 (ptt90) cc_final: 0.7549 (ptt-90) REVERT: J 173 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7591 (ptt-90) REVERT: J 177 ARG cc_start: 0.7729 (ptt90) cc_final: 0.7278 (ptt90) REVERT: J 181 MET cc_start: 0.8458 (mtp) cc_final: 0.8190 (mtp) REVERT: K 32 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7715 (mtt-85) REVERT: L 166 ARG cc_start: 0.8391 (mmt90) cc_final: 0.7956 (mmm160) REVERT: M 113 LYS cc_start: 0.7297 (tppt) cc_final: 0.7045 (mmtm) REVERT: M 153 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7987 (ttmt) REVERT: N 166 ARG cc_start: 0.8416 (mmt90) cc_final: 0.8100 (mmm160) REVERT: N 177 ARG cc_start: 0.7001 (mtm180) cc_final: 0.6260 (ptt90) outliers start: 47 outliers final: 14 residues processed: 500 average time/residue: 0.1832 time to fit residues: 127.9860 Evaluate side-chains 395 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 380 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 128 GLN A 145 HIS B 46 ASN B 86 ASN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 127 HIS E 46 ASN E 86 ASN E 127 HIS F 46 ASN F 127 HIS G 46 ASN ** G 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN H 127 HIS I 46 ASN ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 GLN J 46 ASN J 127 HIS K 46 ASN L 46 ASN L 51 GLN ** L 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 ASN ** M 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN N 86 ASN N 128 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096974 restraints weight = 27505.618| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.63 r_work: 0.3137 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 20006 Z= 0.342 Angle : 0.748 8.947 26936 Z= 0.382 Chirality : 0.050 0.149 3080 Planarity : 0.005 0.046 3486 Dihedral : 4.901 22.508 2660 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.07 % Allowed : 13.87 % Favored : 84.06 % 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 aren not related in a simple way. whole: 0.67 (0.17), residues: 2408 helix: 1.09 (0.15), residues: 1260 sheet: 0.12 (0.33), residues: 224 loop : -0.25 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 177 TYR 0.028 0.003 TYR D 82 PHE 0.046 0.003 PHE F 54 HIS 0.012 0.002 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00793 (20006) covalent geometry : angle 0.74756 (26936) hydrogen bonds : bond 0.04833 ( 1022) hydrogen bonds : angle 4.60334 ( 3360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 381 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8542 (tmm-80) cc_final: 0.8309 (ttp80) REVERT: A 177 ARG cc_start: 0.7507 (ptt90) cc_final: 0.7262 (ptt90) REVERT: B 30 LYS cc_start: 0.9193 (tppt) cc_final: 0.8925 (tppt) REVERT: B 153 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8179 (ttmt) REVERT: B 172 GLU cc_start: 0.8453 (tt0) cc_final: 0.8103 (mt-10) REVERT: B 177 ARG cc_start: 0.7669 (ptt90) cc_final: 0.7308 (ptt90) REVERT: B 181 MET cc_start: 0.8612 (mtp) cc_final: 0.8382 (mtm) REVERT: C 23 ASP cc_start: 0.6642 (p0) cc_final: 0.6281 (p0) REVERT: C 173 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8155 (ttp-170) REVERT: C 177 ARG cc_start: 0.7806 (ptt180) cc_final: 0.7314 (ptt90) REVERT: D 79 MET cc_start: 0.8851 (mmm) cc_final: 0.8497 (mmt) REVERT: D 151 LYS cc_start: 0.8251 (mttt) cc_final: 0.8048 (mmtp) REVERT: D 173 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8013 (tmm-80) REVERT: D 177 ARG cc_start: 0.7777 (ptt90) cc_final: 0.7498 (ptt90) REVERT: D 181 MET cc_start: 0.8516 (mtp) cc_final: 0.8261 (mtp) REVERT: E 172 GLU cc_start: 0.8419 (tt0) cc_final: 0.7955 (mt-10) REVERT: E 177 ARG cc_start: 0.7859 (ptt90) cc_final: 0.7417 (ptt90) REVERT: F 40 VAL cc_start: 0.8230 (t) cc_final: 0.7863 (p) REVERT: F 172 GLU cc_start: 0.8613 (tt0) cc_final: 0.8404 (tt0) REVERT: G 173 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8171 (ttp80) REVERT: G 177 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6905 (ptt90) REVERT: G 181 MET cc_start: 0.8469 (mtp) cc_final: 0.8166 (mtp) REVERT: H 113 LYS cc_start: 0.7905 (tppt) cc_final: 0.7666 (mmtm) REVERT: H 172 GLU cc_start: 0.8445 (tt0) cc_final: 0.8009 (mt-10) REVERT: H 173 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.8263 (ttp80) REVERT: I 79 MET cc_start: 0.8809 (mmm) cc_final: 0.8444 (mmt) REVERT: I 173 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.7834 (ptt-90) REVERT: J 153 LYS cc_start: 0.8522 (tttm) cc_final: 0.8303 (ttmm) REVERT: J 173 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7877 (ptp90) REVERT: J 177 ARG cc_start: 0.7813 (ptt90) cc_final: 0.7239 (ptt90) REVERT: K 32 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7997 (mtt-85) REVERT: K 43 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: K 82 TYR cc_start: 0.8679 (t80) cc_final: 0.8362 (t80) REVERT: K 172 GLU cc_start: 0.8487 (tt0) cc_final: 0.8220 (mt-10) REVERT: K 177 ARG cc_start: 0.7804 (ptt90) cc_final: 0.7558 (ptt90) REVERT: L 23 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6459 (p0) REVERT: L 79 MET cc_start: 0.8940 (mmm) cc_final: 0.8672 (mmm) REVERT: L 166 ARG cc_start: 0.8603 (mmt90) cc_final: 0.8228 (mmm160) REVERT: L 177 ARG cc_start: 0.7566 (ptt90) cc_final: 0.7183 (ptt90) REVERT: M 113 LYS cc_start: 0.7991 (tppt) cc_final: 0.7703 (mmtm) REVERT: M 172 GLU cc_start: 0.8313 (tt0) cc_final: 0.8010 (mt-10) REVERT: M 173 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.7666 (ptt-90) REVERT: N 13 GLU cc_start: 0.7704 (tt0) cc_final: 0.7454 (tt0) REVERT: N 177 ARG cc_start: 0.7404 (mtm180) cc_final: 0.6792 (ptt180) outliers start: 45 outliers final: 24 residues processed: 405 average time/residue: 0.2075 time to fit residues: 114.0028 Evaluate side-chains 361 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 335 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 198 optimal weight: 0.2980 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 86 ASN B 127 HIS E 46 ASN E 86 ASN F 46 ASN F 145 HIS G 46 ASN G 145 HIS H 46 ASN J 46 ASN K 86 ASN K 127 HIS L 46 ASN M 86 ASN M 128 GLN N 86 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102514 restraints weight = 26727.463| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.66 r_work: 0.3228 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20006 Z= 0.138 Angle : 0.580 6.601 26936 Z= 0.293 Chirality : 0.043 0.150 3080 Planarity : 0.004 0.034 3486 Dihedral : 4.521 25.079 2660 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 14.42 % Favored : 83.78 % 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 aren not related in a simple way. whole: 0.83 (0.17), residues: 2408 helix: 1.33 (0.15), residues: 1260 sheet: 0.21 (0.35), residues: 196 loop : -0.34 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 173 TYR 0.026 0.002 TYR H 82 PHE 0.039 0.002 PHE F 54 HIS 0.004 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00313 (20006) covalent geometry : angle 0.57986 (26936) hydrogen bonds : bond 0.03766 ( 1022) hydrogen bonds : angle 4.19162 ( 3360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 397 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6635 (p0) cc_final: 0.6423 (p0) REVERT: A 79 MET cc_start: 0.8892 (mmm) cc_final: 0.8542 (mmm) REVERT: A 86 ASN cc_start: 0.8552 (m-40) cc_final: 0.8281 (m110) REVERT: A 173 ARG cc_start: 0.8544 (tmm-80) cc_final: 0.8306 (ttp80) REVERT: B 30 LYS cc_start: 0.9167 (tppt) cc_final: 0.8914 (tppt) REVERT: B 40 VAL cc_start: 0.7997 (t) cc_final: 0.7583 (p) REVERT: B 153 LYS cc_start: 0.8306 (ttmm) cc_final: 0.8031 (ttmt) REVERT: B 172 GLU cc_start: 0.8465 (tt0) cc_final: 0.8083 (mt-10) REVERT: B 177 ARG cc_start: 0.7691 (ptt90) cc_final: 0.7483 (ptt90) REVERT: C 23 ASP cc_start: 0.6287 (p0) cc_final: 0.5853 (p0) REVERT: C 172 GLU cc_start: 0.8401 (tt0) cc_final: 0.8012 (mt-10) REVERT: C 173 ARG cc_start: 0.8448 (ttp80) cc_final: 0.7661 (ptt-90) REVERT: C 177 ARG cc_start: 0.7844 (ptt180) cc_final: 0.7372 (ptt90) REVERT: D 79 MET cc_start: 0.8752 (mmm) cc_final: 0.8403 (mmt) REVERT: D 173 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8039 (tmm-80) REVERT: D 177 ARG cc_start: 0.7713 (ptt90) cc_final: 0.7429 (ptt90) REVERT: E 46 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7818 (t0) REVERT: E 172 GLU cc_start: 0.8381 (tt0) cc_final: 0.8007 (mt-10) REVERT: E 177 ARG cc_start: 0.7761 (ptt90) cc_final: 0.7292 (ptt90) REVERT: F 13 GLU cc_start: 0.7935 (tt0) cc_final: 0.7682 (tt0) REVERT: F 40 VAL cc_start: 0.8171 (t) cc_final: 0.7868 (p) REVERT: F 56 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: F 79 MET cc_start: 0.8899 (mmm) cc_final: 0.8428 (mmm) REVERT: F 172 GLU cc_start: 0.8550 (tt0) cc_final: 0.8284 (mt-10) REVERT: F 173 ARG cc_start: 0.8485 (ttp80) cc_final: 0.7802 (ptt-90) REVERT: G 173 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8024 (tmm-80) REVERT: G 177 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6847 (ptt90) REVERT: G 181 MET cc_start: 0.8521 (mtp) cc_final: 0.8311 (mtm) REVERT: H 46 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7754 (t0) REVERT: H 113 LYS cc_start: 0.7945 (tppt) cc_final: 0.7721 (mmtm) REVERT: H 173 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.8331 (ttp80) REVERT: I 79 MET cc_start: 0.8686 (mmm) cc_final: 0.8265 (mmt) REVERT: I 172 GLU cc_start: 0.8500 (tt0) cc_final: 0.8149 (mt-10) REVERT: I 173 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7442 (ptt90) REVERT: J 173 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7887 (ptt-90) REVERT: J 177 ARG cc_start: 0.7861 (ptt90) cc_final: 0.7287 (ptt90) REVERT: K 32 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7786 (mtt-85) REVERT: K 172 GLU cc_start: 0.8464 (tt0) cc_final: 0.8118 (mt-10) REVERT: K 173 ARG cc_start: 0.8301 (ptt90) cc_final: 0.8031 (ttp-110) REVERT: K 177 ARG cc_start: 0.7766 (ptt90) cc_final: 0.7402 (ptt90) REVERT: L 23 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.6134 (p0) REVERT: L 46 ASN cc_start: 0.8274 (m110) cc_final: 0.7896 (m110) REVERT: L 79 MET cc_start: 0.8832 (mmm) cc_final: 0.8522 (mmm) REVERT: L 166 ARG cc_start: 0.8590 (mmt90) cc_final: 0.8277 (mmm160) REVERT: L 177 ARG cc_start: 0.7527 (ptt90) cc_final: 0.7175 (ptt90) REVERT: M 40 VAL cc_start: 0.8080 (t) cc_final: 0.7632 (p) REVERT: M 113 LYS cc_start: 0.7946 (tppt) cc_final: 0.7638 (mmtm) REVERT: M 172 GLU cc_start: 0.8259 (tt0) cc_final: 0.7920 (mt-10) REVERT: M 173 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.7556 (ptt-90) REVERT: M 177 ARG cc_start: 0.7696 (ptt90) cc_final: 0.7415 (ptt90) REVERT: N 172 GLU cc_start: 0.8426 (tt0) cc_final: 0.8171 (mt-10) REVERT: N 173 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7768 (ptt-90) REVERT: N 177 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6574 (ptt90) outliers start: 39 outliers final: 13 residues processed: 418 average time/residue: 0.2050 time to fit residues: 116.9539 Evaluate side-chains 371 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 354 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain M residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 93 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 185 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN C 145 HIS E 46 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN G 46 ASN G 86 ASN G 145 HIS H 46 ASN I 46 ASN J 46 ASN K 86 ASN L 86 ASN M 86 ASN N 46 ASN N 86 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.102446 restraints weight = 26703.670| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.71 r_work: 0.3226 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20006 Z= 0.149 Angle : 0.583 6.211 26936 Z= 0.295 Chirality : 0.043 0.150 3080 Planarity : 0.004 0.050 3486 Dihedral : 4.456 24.959 2660 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.07 % Allowed : 14.70 % Favored : 83.23 % 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 aren not related in a simple way. whole: 0.86 (0.17), residues: 2408 helix: 1.39 (0.15), residues: 1260 sheet: 0.16 (0.35), residues: 196 loop : -0.38 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 177 TYR 0.025 0.002 TYR D 82 PHE 0.038 0.002 PHE C 54 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00344 (20006) covalent geometry : angle 0.58275 (26936) hydrogen bonds : bond 0.03762 ( 1022) hydrogen bonds : angle 4.19180 ( 3360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 376 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6525 (p0) cc_final: 0.6260 (p0) REVERT: A 79 MET cc_start: 0.8899 (mmm) cc_final: 0.8541 (mmm) REVERT: A 86 ASN cc_start: 0.8512 (m-40) cc_final: 0.8227 (m-40) REVERT: A 172 GLU cc_start: 0.8322 (tt0) cc_final: 0.7935 (mt-10) REVERT: A 173 ARG cc_start: 0.8595 (tmm-80) cc_final: 0.8348 (ttp80) REVERT: B 30 LYS cc_start: 0.9163 (tppt) cc_final: 0.8903 (tppt) REVERT: B 166 ARG cc_start: 0.8660 (mmt90) cc_final: 0.8212 (mmm160) REVERT: B 172 GLU cc_start: 0.8458 (tt0) cc_final: 0.8068 (mt-10) REVERT: C 172 GLU cc_start: 0.8349 (tt0) cc_final: 0.7916 (mt-10) REVERT: C 173 ARG cc_start: 0.8538 (ttp80) cc_final: 0.7935 (ptt-90) REVERT: C 177 ARG cc_start: 0.7756 (ptt180) cc_final: 0.7289 (ptt90) REVERT: D 56 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: D 79 MET cc_start: 0.8688 (mmm) cc_final: 0.8440 (mmt) REVERT: D 173 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8224 (tmm-80) REVERT: D 177 ARG cc_start: 0.7652 (ptt90) cc_final: 0.7393 (ptt90) REVERT: E 173 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8354 (tmm-80) REVERT: E 177 ARG cc_start: 0.7709 (ptt90) cc_final: 0.7328 (ptt90) REVERT: F 13 GLU cc_start: 0.7898 (tt0) cc_final: 0.7621 (tt0) REVERT: F 56 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: F 172 GLU cc_start: 0.8517 (tt0) cc_final: 0.8220 (mt-10) REVERT: F 173 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7864 (ptt-90) REVERT: F 177 ARG cc_start: 0.7566 (ptt90) cc_final: 0.7151 (ptt90) REVERT: G 173 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8081 (tmm-80) REVERT: G 177 ARG cc_start: 0.7320 (mtm180) cc_final: 0.6838 (ptt90) REVERT: G 181 MET cc_start: 0.8552 (mtp) cc_final: 0.8323 (mtm) REVERT: H 113 LYS cc_start: 0.8103 (tppt) cc_final: 0.7872 (mmtm) REVERT: H 177 ARG cc_start: 0.7711 (ptt90) cc_final: 0.7289 (ptt90) REVERT: I 79 MET cc_start: 0.8638 (mmm) cc_final: 0.8342 (mmt) REVERT: I 172 GLU cc_start: 0.8443 (tt0) cc_final: 0.8116 (mt-10) REVERT: I 173 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: J 173 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7948 (ptt-90) REVERT: K 19 GLU cc_start: 0.6642 (mp0) cc_final: 0.6433 (mp0) REVERT: K 32 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7737 (mtt-85) REVERT: K 172 GLU cc_start: 0.8469 (tt0) cc_final: 0.8075 (mt-10) REVERT: K 177 ARG cc_start: 0.7748 (ptt90) cc_final: 0.7290 (ptt90) REVERT: L 23 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.6100 (p0) REVERT: L 166 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8272 (mmm160) REVERT: L 177 ARG cc_start: 0.7577 (ptt90) cc_final: 0.7289 (ptt90) REVERT: M 40 VAL cc_start: 0.7987 (t) cc_final: 0.7543 (p) REVERT: M 113 LYS cc_start: 0.7986 (tppt) cc_final: 0.7684 (mmtm) REVERT: M 172 GLU cc_start: 0.8266 (tt0) cc_final: 0.7923 (mt-10) REVERT: M 173 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.7607 (ptt-90) REVERT: M 177 ARG cc_start: 0.7774 (ptt90) cc_final: 0.7487 (ptt90) REVERT: N 172 GLU cc_start: 0.8447 (tt0) cc_final: 0.8154 (mt-10) REVERT: N 173 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7808 (ptt-90) REVERT: N 177 ARG cc_start: 0.7284 (mtm180) cc_final: 0.6666 (ptt90) outliers start: 45 outliers final: 20 residues processed: 399 average time/residue: 0.2057 time to fit residues: 112.3122 Evaluate side-chains 373 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 350 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 86 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 0.0030 chunk 191 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN C 86 ASN C 128 GLN C 145 HIS E 46 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN G 145 HIS H 46 ASN I 127 HIS ** I 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN K 86 ASN M 86 ASN N 86 ASN N 127 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101637 restraints weight = 26646.843| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.62 r_work: 0.3212 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20006 Z= 0.180 Angle : 0.599 6.839 26936 Z= 0.302 Chirality : 0.044 0.148 3080 Planarity : 0.004 0.034 3486 Dihedral : 4.480 24.753 2660 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.03 % Allowed : 15.85 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2408 helix: 1.38 (0.15), residues: 1260 sheet: -0.06 (0.34), residues: 196 loop : -0.48 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 173 TYR 0.024 0.002 TYR I 82 PHE 0.038 0.002 PHE D 54 HIS 0.004 0.001 HIS M 145 Details of bonding type rmsd covalent geometry : bond 0.00419 (20006) covalent geometry : angle 0.59901 (26936) hydrogen bonds : bond 0.03864 ( 1022) hydrogen bonds : angle 4.24664 ( 3360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 367 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7639 (tp30) cc_final: 0.7406 (tp30) REVERT: A 86 ASN cc_start: 0.8530 (m-40) cc_final: 0.8234 (m110) REVERT: A 172 GLU cc_start: 0.8294 (tt0) cc_final: 0.7996 (mt-10) REVERT: B 30 LYS cc_start: 0.9222 (tppt) cc_final: 0.8975 (tppt) REVERT: B 86 ASN cc_start: 0.8310 (m-40) cc_final: 0.7818 (m110) REVERT: B 166 ARG cc_start: 0.8792 (mmt90) cc_final: 0.8349 (mmm160) REVERT: B 172 GLU cc_start: 0.8406 (tt0) cc_final: 0.8204 (mt-10) REVERT: B 173 ARG cc_start: 0.8413 (ttp80) cc_final: 0.7804 (ptt-90) REVERT: B 177 ARG cc_start: 0.7946 (ptt90) cc_final: 0.7701 (ptt90) REVERT: C 168 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8348 (tp) REVERT: C 172 GLU cc_start: 0.8339 (tt0) cc_final: 0.7900 (mt-10) REVERT: C 173 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7975 (ptt-90) REVERT: C 177 ARG cc_start: 0.7768 (ptt180) cc_final: 0.7308 (ptt90) REVERT: D 56 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: D 79 MET cc_start: 0.8696 (mmm) cc_final: 0.8486 (mmt) REVERT: E 173 ARG cc_start: 0.8563 (tmm-80) cc_final: 0.8297 (tmm-80) REVERT: F 40 VAL cc_start: 0.8247 (t) cc_final: 0.7890 (p) REVERT: F 56 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: F 166 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8203 (mmm160) REVERT: F 173 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7886 (ptt-90) REVERT: F 177 ARG cc_start: 0.7632 (ptt90) cc_final: 0.7217 (ptt90) REVERT: G 173 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8057 (tmm-80) REVERT: G 177 ARG cc_start: 0.7426 (mtm180) cc_final: 0.6919 (ptt90) REVERT: H 113 LYS cc_start: 0.8077 (tppt) cc_final: 0.7846 (mmtm) REVERT: H 173 ARG cc_start: 0.8513 (tmm-80) cc_final: 0.8260 (ttp80) REVERT: H 177 ARG cc_start: 0.7692 (ptt90) cc_final: 0.7305 (ptt90) REVERT: I 79 MET cc_start: 0.8746 (mmm) cc_final: 0.8467 (mmm) REVERT: I 151 LYS cc_start: 0.8315 (tttm) cc_final: 0.7585 (ttpp) REVERT: I 172 GLU cc_start: 0.8441 (tt0) cc_final: 0.8181 (mt-10) REVERT: I 173 ARG cc_start: 0.8369 (ttp-110) cc_final: 0.8085 (ttp-110) REVERT: J 46 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7802 (t0) REVERT: J 173 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8142 (tmm-80) REVERT: J 177 ARG cc_start: 0.7654 (ptt180) cc_final: 0.7337 (ptt90) REVERT: K 168 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8338 (tt) REVERT: K 173 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7490 (ptt90) REVERT: K 177 ARG cc_start: 0.7748 (ptt90) cc_final: 0.7314 (ptt90) REVERT: L 23 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6428 (p0) REVERT: L 46 ASN cc_start: 0.8214 (m110) cc_final: 0.7869 (m110) REVERT: L 166 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8384 (mmm160) REVERT: L 177 ARG cc_start: 0.7603 (ptt90) cc_final: 0.7286 (ptt90) REVERT: M 113 LYS cc_start: 0.7970 (tppt) cc_final: 0.7708 (mmtm) REVERT: M 173 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.7856 (ptt-90) REVERT: M 177 ARG cc_start: 0.7764 (ptt90) cc_final: 0.7413 (ptt90) REVERT: N 168 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8052 (tp) REVERT: N 172 GLU cc_start: 0.8463 (tt0) cc_final: 0.8211 (mt-10) REVERT: N 173 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7878 (ptt-90) REVERT: N 177 ARG cc_start: 0.7452 (mtm180) cc_final: 0.6806 (ptt90) outliers start: 44 outliers final: 17 residues processed: 392 average time/residue: 0.2164 time to fit residues: 115.1941 Evaluate side-chains 369 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 345 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 145 HIS D 86 ASN E 46 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS G 46 ASN G 127 HIS G 145 HIS H 46 ASN I 86 ASN J 46 ASN K 86 ASN L 127 HIS M 86 ASN M 127 HIS N 86 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100208 restraints weight = 26932.783| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.64 r_work: 0.3196 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20006 Z= 0.204 Angle : 0.619 7.195 26936 Z= 0.312 Chirality : 0.045 0.156 3080 Planarity : 0.004 0.056 3486 Dihedral : 4.520 24.674 2660 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.71 % Allowed : 16.54 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2408 helix: 1.37 (0.15), residues: 1260 sheet: -0.31 (0.34), residues: 196 loop : -0.58 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 173 TYR 0.027 0.002 TYR I 82 PHE 0.035 0.002 PHE H 54 HIS 0.004 0.001 HIS M 145 Details of bonding type rmsd covalent geometry : bond 0.00475 (20006) covalent geometry : angle 0.61924 (26936) hydrogen bonds : bond 0.03940 ( 1022) hydrogen bonds : angle 4.30613 ( 3360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASN cc_start: 0.8549 (m-40) cc_final: 0.8298 (m110) REVERT: B 30 LYS cc_start: 0.9220 (tppt) cc_final: 0.8988 (tppt) REVERT: B 86 ASN cc_start: 0.8315 (m-40) cc_final: 0.7792 (m110) REVERT: B 166 ARG cc_start: 0.8867 (mmt90) cc_final: 0.8443 (mmm160) REVERT: B 168 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8036 (tp) REVERT: B 172 GLU cc_start: 0.8415 (tt0) cc_final: 0.8208 (mt-10) REVERT: B 173 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8106 (tmm-80) REVERT: B 177 ARG cc_start: 0.7928 (ptt90) cc_final: 0.7696 (ptt90) REVERT: C 151 LYS cc_start: 0.8234 (mttt) cc_final: 0.8011 (mmtp) REVERT: C 168 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8290 (tp) REVERT: C 172 GLU cc_start: 0.8282 (tt0) cc_final: 0.7827 (mt-10) REVERT: C 173 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8239 (tmm-80) REVERT: C 177 ARG cc_start: 0.7812 (ptt180) cc_final: 0.7345 (ptt90) REVERT: D 56 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: D 79 MET cc_start: 0.8757 (mmm) cc_final: 0.8323 (mmm) REVERT: D 177 ARG cc_start: 0.7622 (ptt90) cc_final: 0.7305 (ptt90) REVERT: E 153 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8059 (ttmt) REVERT: E 173 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8266 (tmm-80) REVERT: F 40 VAL cc_start: 0.8255 (t) cc_final: 0.7895 (p) REVERT: F 56 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: F 166 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8164 (mmm160) REVERT: F 172 GLU cc_start: 0.8466 (tt0) cc_final: 0.8255 (mt-10) REVERT: F 173 ARG cc_start: 0.8472 (ttp80) cc_final: 0.7796 (ptt-90) REVERT: G 173 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8073 (tmm-80) REVERT: G 177 ARG cc_start: 0.7455 (mtm180) cc_final: 0.6905 (ptt90) REVERT: H 113 LYS cc_start: 0.8102 (tppt) cc_final: 0.7863 (mmtm) REVERT: H 173 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.8265 (tmm-80) REVERT: I 79 MET cc_start: 0.8797 (mmm) cc_final: 0.8480 (mmt) REVERT: I 172 GLU cc_start: 0.8443 (tt0) cc_final: 0.8176 (mt-10) REVERT: I 173 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8098 (ttp-110) REVERT: J 54 PHE cc_start: 0.8147 (t80) cc_final: 0.7869 (t80) REVERT: J 173 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8195 (tmm-80) REVERT: J 177 ARG cc_start: 0.7662 (ptt180) cc_final: 0.7378 (ptt90) REVERT: K 151 LYS cc_start: 0.8252 (mttt) cc_final: 0.7931 (mmtp) REVERT: K 173 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.7385 (ptt90) REVERT: L 23 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6567 (p0) REVERT: L 166 ARG cc_start: 0.8691 (mmt90) cc_final: 0.8398 (mmm160) REVERT: L 177 ARG cc_start: 0.7635 (ptt90) cc_final: 0.7303 (ptt90) REVERT: M 113 LYS cc_start: 0.7988 (tppt) cc_final: 0.7735 (mmtm) REVERT: M 173 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.7760 (ptt-90) REVERT: M 177 ARG cc_start: 0.7752 (ptt90) cc_final: 0.7333 (ptt90) REVERT: N 168 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7948 (tp) REVERT: N 172 GLU cc_start: 0.8469 (tt0) cc_final: 0.8192 (mt-10) REVERT: N 173 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7879 (ptt-90) REVERT: N 177 ARG cc_start: 0.7479 (mtm180) cc_final: 0.6818 (ptt90) outliers start: 37 outliers final: 18 residues processed: 382 average time/residue: 0.2345 time to fit residues: 120.6795 Evaluate side-chains 367 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 343 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 145 HIS D 86 ASN D 128 GLN E 46 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS G 46 ASN G 145 HIS J 46 ASN N 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098963 restraints weight = 26969.580| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.64 r_work: 0.3173 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20006 Z= 0.242 Angle : 0.653 9.668 26936 Z= 0.330 Chirality : 0.046 0.165 3080 Planarity : 0.004 0.032 3486 Dihedral : 4.630 25.138 2660 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.43 % Allowed : 16.77 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.17), residues: 2408 helix: 1.20 (0.15), residues: 1274 sheet: -0.66 (0.35), residues: 196 loop : -0.59 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 177 TYR 0.033 0.003 TYR I 82 PHE 0.041 0.003 PHE J 54 HIS 0.008 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00564 (20006) covalent geometry : angle 0.65327 (26936) hydrogen bonds : bond 0.04107 ( 1022) hydrogen bonds : angle 4.43250 ( 3360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 355 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7925 (ptt-90) REVERT: B 30 LYS cc_start: 0.9211 (tppt) cc_final: 0.8972 (tppt) REVERT: B 168 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7928 (tp) REVERT: B 172 GLU cc_start: 0.8422 (tt0) cc_final: 0.8173 (mt-10) REVERT: B 177 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7600 (ptt90) REVERT: C 151 LYS cc_start: 0.8283 (mttt) cc_final: 0.7986 (mmtp) REVERT: C 168 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8186 (tp) REVERT: C 172 GLU cc_start: 0.8272 (tt0) cc_final: 0.7787 (mt-10) REVERT: C 173 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8278 (tmm-80) REVERT: C 177 ARG cc_start: 0.7813 (ptt180) cc_final: 0.7361 (ptt90) REVERT: D 56 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: D 151 LYS cc_start: 0.8325 (mttt) cc_final: 0.7968 (mmtp) REVERT: D 173 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.8215 (ttp80) REVERT: D 177 ARG cc_start: 0.7635 (ptt90) cc_final: 0.7320 (ptt90) REVERT: E 173 ARG cc_start: 0.8573 (tmm-80) cc_final: 0.8272 (tmm-80) REVERT: F 40 VAL cc_start: 0.8249 (t) cc_final: 0.7888 (p) REVERT: F 56 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: F 166 ARG cc_start: 0.8764 (mmt90) cc_final: 0.8163 (mmm160) REVERT: F 173 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7816 (ptt-90) REVERT: G 173 ARG cc_start: 0.8436 (ttp-110) cc_final: 0.8076 (tmm-80) REVERT: G 177 ARG cc_start: 0.7295 (mtm180) cc_final: 0.6897 (ptt180) REVERT: H 113 LYS cc_start: 0.7986 (tppt) cc_final: 0.7739 (mmtm) REVERT: H 173 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8268 (tmm-80) REVERT: I 79 MET cc_start: 0.8846 (mmm) cc_final: 0.8529 (mmt) REVERT: I 151 LYS cc_start: 0.8318 (tttm) cc_final: 0.7642 (ttpp) REVERT: I 172 GLU cc_start: 0.8478 (tt0) cc_final: 0.8166 (mt-10) REVERT: I 173 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.7918 (ttp-110) REVERT: J 46 ASN cc_start: 0.8140 (t160) cc_final: 0.7863 (t0) REVERT: J 173 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8222 (tmm-80) REVERT: J 177 ARG cc_start: 0.7613 (ptt180) cc_final: 0.7301 (ptt90) REVERT: K 86 ASN cc_start: 0.8404 (m-40) cc_final: 0.7874 (m110) REVERT: K 151 LYS cc_start: 0.8282 (mttt) cc_final: 0.7845 (mmtp) REVERT: K 172 GLU cc_start: 0.8419 (tt0) cc_final: 0.8013 (mt-10) REVERT: K 173 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.7398 (ptt90) REVERT: L 23 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6745 (p0) REVERT: L 46 ASN cc_start: 0.8373 (m-40) cc_final: 0.7871 (m-40) REVERT: L 151 LYS cc_start: 0.8368 (mttt) cc_final: 0.8088 (mmtp) REVERT: L 166 ARG cc_start: 0.8685 (mmt90) cc_final: 0.8380 (mmm160) REVERT: L 177 ARG cc_start: 0.7612 (ptt90) cc_final: 0.7268 (ptt90) REVERT: M 113 LYS cc_start: 0.8013 (tppt) cc_final: 0.7746 (mmtm) REVERT: M 173 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.7747 (ptt-90) REVERT: M 177 ARG cc_start: 0.7758 (ptt90) cc_final: 0.7368 (ptt90) REVERT: N 168 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7856 (tp) REVERT: N 172 GLU cc_start: 0.8396 (tt0) cc_final: 0.8118 (mt-10) REVERT: N 177 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6952 (ptt180) outliers start: 31 outliers final: 16 residues processed: 369 average time/residue: 0.2413 time to fit residues: 119.4991 Evaluate side-chains 366 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 344 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 225 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 86 ASN C 46 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS D 86 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN H 46 ASN I 145 HIS K 86 ASN L 46 ASN N 46 ASN N 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103298 restraints weight = 26450.675| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.69 r_work: 0.3240 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20006 Z= 0.136 Angle : 0.596 8.938 26936 Z= 0.300 Chirality : 0.044 0.186 3080 Planarity : 0.004 0.032 3486 Dihedral : 4.456 24.977 2660 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.20 % Allowed : 17.42 % Favored : 81.38 % 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 aren not related in a simple way. whole: 0.66 (0.17), residues: 2408 helix: 1.33 (0.15), residues: 1274 sheet: -0.52 (0.34), residues: 196 loop : -0.52 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.032 0.002 TYR B 82 PHE 0.033 0.002 PHE G 54 HIS 0.013 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00314 (20006) covalent geometry : angle 0.59603 (26936) hydrogen bonds : bond 0.03633 ( 1022) hydrogen bonds : angle 4.28241 ( 3360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 372 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8385 (ttp80) cc_final: 0.7897 (ptt-90) REVERT: B 30 LYS cc_start: 0.9180 (tppt) cc_final: 0.8948 (tppt) REVERT: B 166 ARG cc_start: 0.8825 (mmt90) cc_final: 0.8408 (mmm160) REVERT: B 168 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8165 (tp) REVERT: B 172 GLU cc_start: 0.8446 (tt0) cc_final: 0.8058 (mt-10) REVERT: B 173 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8118 (tmm-80) REVERT: B 177 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7632 (ptt90) REVERT: C 168 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 172 GLU cc_start: 0.8232 (tt0) cc_final: 0.7735 (mt-10) REVERT: C 173 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8105 (ptt-90) REVERT: C 177 ARG cc_start: 0.7733 (ptt180) cc_final: 0.7278 (ptt90) REVERT: D 56 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: D 79 MET cc_start: 0.8705 (mmm) cc_final: 0.8433 (mmt) REVERT: D 173 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8252 (ttp80) REVERT: D 177 ARG cc_start: 0.7452 (ptt90) cc_final: 0.7160 (ptt90) REVERT: E 173 ARG cc_start: 0.8586 (tmm-80) cc_final: 0.8375 (tmm-80) REVERT: E 181 MET cc_start: 0.8422 (mtm) cc_final: 0.8134 (mtm) REVERT: F 40 VAL cc_start: 0.8203 (t) cc_final: 0.7866 (p) REVERT: F 56 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: F 79 MET cc_start: 0.8899 (mmm) cc_final: 0.8684 (mmm) REVERT: F 166 ARG cc_start: 0.8659 (mmt90) cc_final: 0.8115 (mmm160) REVERT: F 173 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7858 (ptt-90) REVERT: G 166 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8360 (mmm160) REVERT: G 173 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8008 (tmm-80) REVERT: G 177 ARG cc_start: 0.7366 (mtm180) cc_final: 0.6925 (ptt180) REVERT: H 113 LYS cc_start: 0.8097 (tppt) cc_final: 0.7885 (mmtm) REVERT: H 173 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8320 (tmm-80) REVERT: I 79 MET cc_start: 0.8740 (mmm) cc_final: 0.8322 (mmm) REVERT: I 125 MET cc_start: 0.7887 (ttt) cc_final: 0.7674 (ttt) REVERT: I 151 LYS cc_start: 0.8297 (tttm) cc_final: 0.7921 (ttpp) REVERT: I 172 GLU cc_start: 0.8440 (tt0) cc_final: 0.8185 (mt-10) REVERT: I 173 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8102 (ttp-110) REVERT: J 82 TYR cc_start: 0.8341 (t80) cc_final: 0.8020 (t80) REVERT: J 173 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8166 (tmm-80) REVERT: K 166 ARG cc_start: 0.8877 (mmt90) cc_final: 0.8522 (mmm160) REVERT: K 173 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.7335 (ptt90) REVERT: L 23 ASP cc_start: 0.6573 (p0) cc_final: 0.6340 (p0) REVERT: L 166 ARG cc_start: 0.8659 (mmt90) cc_final: 0.8380 (mmm160) REVERT: L 177 ARG cc_start: 0.7601 (ptt90) cc_final: 0.7257 (ptt90) REVERT: M 113 LYS cc_start: 0.8150 (tppt) cc_final: 0.7881 (mmtm) REVERT: M 173 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.7700 (ptt-90) REVERT: M 177 ARG cc_start: 0.7692 (ptt90) cc_final: 0.7300 (ptt90) REVERT: N 168 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7907 (tp) REVERT: N 172 GLU cc_start: 0.8460 (tt0) cc_final: 0.8142 (mt-10) REVERT: N 173 ARG cc_start: 0.8464 (ttp80) cc_final: 0.7789 (ptt-90) REVERT: N 177 ARG cc_start: 0.7417 (mtm180) cc_final: 0.6945 (ptt180) outliers start: 26 outliers final: 11 residues processed: 389 average time/residue: 0.2112 time to fit residues: 111.1030 Evaluate side-chains 362 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 346 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN H 86 ASN K 86 ASN N 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101782 restraints weight = 27216.498| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.65 r_work: 0.3237 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20006 Z= 0.136 Angle : 0.606 8.890 26936 Z= 0.303 Chirality : 0.044 0.155 3080 Planarity : 0.004 0.033 3486 Dihedral : 4.415 24.239 2660 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.92 % Allowed : 17.88 % Favored : 81.20 % 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 aren not related in a simple way. whole: 0.70 (0.17), residues: 2408 helix: 1.37 (0.15), residues: 1274 sheet: -0.46 (0.33), residues: 196 loop : -0.51 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 177 TYR 0.034 0.002 TYR B 82 PHE 0.033 0.002 PHE M 54 HIS 0.011 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00313 (20006) covalent geometry : angle 0.60558 (26936) hydrogen bonds : bond 0.03619 ( 1022) hydrogen bonds : angle 4.25424 ( 3360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 361 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 LYS cc_start: 0.9237 (tppt) cc_final: 0.9023 (tppt) REVERT: B 166 ARG cc_start: 0.8842 (mmt90) cc_final: 0.8446 (mmm160) REVERT: B 168 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 172 GLU cc_start: 0.8448 (tt0) cc_final: 0.8136 (mt-10) REVERT: B 173 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8107 (tmm-80) REVERT: B 177 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7644 (ptt90) REVERT: C 168 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8259 (tp) REVERT: C 172 GLU cc_start: 0.8231 (tt0) cc_final: 0.7771 (mt-10) REVERT: C 173 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8095 (ptt-90) REVERT: C 177 ARG cc_start: 0.7799 (ptt180) cc_final: 0.7381 (ptt90) REVERT: D 19 GLU cc_start: 0.6737 (mp0) cc_final: 0.6190 (mp0) REVERT: D 79 MET cc_start: 0.8658 (mmm) cc_final: 0.8396 (mmt) REVERT: D 173 ARG cc_start: 0.8494 (tmm-80) cc_final: 0.8141 (ttp80) REVERT: D 177 ARG cc_start: 0.7462 (ptt90) cc_final: 0.7135 (ptt90) REVERT: E 181 MET cc_start: 0.8338 (mtm) cc_final: 0.8026 (mtm) REVERT: F 40 VAL cc_start: 0.8314 (t) cc_final: 0.7963 (p) REVERT: F 113 LYS cc_start: 0.7537 (tppt) cc_final: 0.7290 (mmtt) REVERT: F 166 ARG cc_start: 0.8743 (mmt90) cc_final: 0.8252 (mmm160) REVERT: F 173 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7821 (ptt-90) REVERT: G 166 ARG cc_start: 0.8763 (mmt90) cc_final: 0.8477 (mmm160) REVERT: G 173 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.7911 (tmm-80) REVERT: H 113 LYS cc_start: 0.8069 (tppt) cc_final: 0.7846 (mmtm) REVERT: I 79 MET cc_start: 0.8685 (mmm) cc_final: 0.8392 (mmm) REVERT: I 125 MET cc_start: 0.7942 (ttt) cc_final: 0.7727 (ttt) REVERT: I 151 LYS cc_start: 0.8284 (tttm) cc_final: 0.7899 (ttpp) REVERT: I 172 GLU cc_start: 0.8462 (tt0) cc_final: 0.8258 (mt-10) REVERT: I 173 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.8048 (ttp-110) REVERT: J 82 TYR cc_start: 0.8386 (t80) cc_final: 0.8041 (t80) REVERT: J 173 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8098 (tmm-80) REVERT: K 86 ASN cc_start: 0.8142 (m-40) cc_final: 0.7624 (m110) REVERT: K 168 LEU cc_start: 0.8334 (tt) cc_final: 0.7814 (tp) REVERT: K 173 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7325 (ptt90) REVERT: K 177 ARG cc_start: 0.7750 (ptt180) cc_final: 0.6725 (ptt-90) REVERT: L 23 ASP cc_start: 0.6666 (p0) cc_final: 0.6442 (p0) REVERT: L 46 ASN cc_start: 0.8098 (m110) cc_final: 0.7795 (m110) REVERT: L 166 ARG cc_start: 0.8721 (mmt90) cc_final: 0.8464 (mmm160) REVERT: L 173 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8063 (ptt-90) REVERT: L 177 ARG cc_start: 0.7706 (ptt90) cc_final: 0.7375 (ptt90) REVERT: M 113 LYS cc_start: 0.8097 (tppt) cc_final: 0.7851 (mmtm) REVERT: M 173 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.7678 (ptt-90) REVERT: M 177 ARG cc_start: 0.7726 (ptt90) cc_final: 0.7375 (ptt90) REVERT: N 168 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7965 (tp) REVERT: N 172 GLU cc_start: 0.8499 (tt0) cc_final: 0.8190 (mt-10) REVERT: N 173 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7778 (ptt-90) REVERT: N 177 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7061 (ptt180) outliers start: 20 outliers final: 12 residues processed: 373 average time/residue: 0.2292 time to fit residues: 115.5157 Evaluate side-chains 364 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 349 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 73 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 233 optimal weight: 0.0570 chunk 63 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 0.0070 chunk 159 optimal weight: 0.0970 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN H 86 ASN J 46 ASN K 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106498 restraints weight = 26427.279| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.64 r_work: 0.3295 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20006 Z= 0.120 Angle : 0.609 10.594 26936 Z= 0.304 Chirality : 0.043 0.162 3080 Planarity : 0.004 0.034 3486 Dihedral : 4.358 23.827 2660 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.74 % Allowed : 17.88 % Favored : 81.38 % 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 aren not related in a simple way. whole: 0.75 (0.17), residues: 2408 helix: 1.38 (0.15), residues: 1274 sheet: -0.28 (0.33), residues: 196 loop : -0.48 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 177 TYR 0.035 0.002 TYR B 82 PHE 0.033 0.002 PHE F 54 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00272 (20006) covalent geometry : angle 0.60891 (26936) hydrogen bonds : bond 0.03459 ( 1022) hydrogen bonds : angle 4.18243 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4714.63 seconds wall clock time: 81 minutes 40.81 seconds (4900.81 seconds total)