Starting phenix.real_space_refine on Thu Mar 14 21:34:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/03_2024/6vx4_21429.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/03_2024/6vx4_21429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/03_2024/6vx4_21429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/03_2024/6vx4_21429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/03_2024/6vx4_21429.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/03_2024/6vx4_21429.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.003 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 41 5.16 5 C 6239 2.51 5 N 1659 2.21 5 O 1874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 99": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9813 Number of models: 1 Model: "" Number of chains: 9 Chain: "K" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 781 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1769 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain: "F" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1908 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Time building chain proxies: 5.44, per 1000 atoms: 0.55 Number of scatterers: 9813 At special positions: 0 Unit cell: (83.64, 86.1, 136.53, 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 41 16.00 O 1874 8.00 N 1659 7.00 C 6239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 133 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS F 269 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 19.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.717A pdb=" N ASP C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.667A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.906A pdb=" N ASP A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 96 removed outlier: 3.770A pdb=" N ASP B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.601A pdb=" N ASP D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 81 through 96 removed outlier: 3.548A pdb=" N ASP E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR E 91 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 117 Processing helix chain 'G' and resid 29 through 37 Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.508A pdb=" N SER G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 84 removed outlier: 3.652A pdb=" N THR G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 207 through 213 removed outlier: 6.711A pdb=" N ILE G 210 " --> pdb=" O CYS G 207 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLY G 211 " --> pdb=" O PHE G 208 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 213 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 241 removed outlier: 3.631A pdb=" N SER G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 47 through 54 removed outlier: 3.555A pdb=" N GLN F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.715A pdb=" N THR F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.525A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.564A pdb=" N SER K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 46 removed outlier: 4.928A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU C 125 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS C 102 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 122 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS C 70 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLY C 124 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 12.787A pdb=" N VAL C 72 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 16.935A pdb=" N SER C 126 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 58 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE C 39 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN C 46 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N VAL E 123 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 101 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER E 35 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 103 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR E 33 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 121 through 126 removed outlier: 8.545A pdb=" N VAL C 123 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 46 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 56 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 42 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS A 54 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 44 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 52 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 46 removed outlier: 5.113A pdb=" N TYR A 33 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 103 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER A 35 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 101 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU A 125 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A 102 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A 123 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 46 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE B 39 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 58 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 46 removed outlier: 4.856A pdb=" N TYR B 33 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 103 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B 35 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 101 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 100 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU B 125 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS B 102 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL B 123 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D 46 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE D 39 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 58 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 46 removed outlier: 5.368A pdb=" N TYR D 33 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 103 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER D 35 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 101 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 124 " --> pdb=" O HIS D 102 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL D 123 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 46 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 56 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU E 42 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS E 54 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL E 44 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR E 52 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.653A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.563A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE H 59 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.540A pdb=" N PHE H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.969A pdb=" N LEU G 92 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 147 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG G 98 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE G 145 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.549A pdb=" N ASP G 26 " --> pdb=" O TYR G 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR G 93 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 92 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 147 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG G 98 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE G 145 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 103 through 105 Processing sheet with id=AB5, first strand: chain 'G' and resid 204 through 205 Processing sheet with id=AB6, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.582A pdb=" N ASP F 91 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET F 30 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLN F 65 " --> pdb=" O MET F 30 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP F 32 " --> pdb=" O GLN F 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 85 removed outlier: 5.616A pdb=" N PHE F 84 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 147 " --> pdb=" O THR F 158 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP F 190 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F 238 " --> pdb=" O TRP F 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 234 " --> pdb=" O GLY F 194 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 906 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: 2.86 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3152 1.34 - 1.46: 2429 1.46 - 1.58: 4424 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 10059 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" CA TYR G 95 " pdb=" C TYR G 95 " ideal model delta sigma weight residual 1.526 1.513 0.013 1.22e-02 6.72e+03 1.09e+00 bond pdb=" CA ILE F 88 " pdb=" CB ILE F 88 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 1.02e+00 bond pdb=" CA ILE G 197 " pdb=" CB ILE G 197 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.73e-01 bond pdb=" N PHE A 117 " pdb=" CA PHE A 117 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 7.32e-01 ... (remaining 10054 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 316 107.17 - 113.87: 5562 113.87 - 120.58: 3669 120.58 - 127.28: 4026 127.28 - 133.99: 129 Bond angle restraints: 13702 Sorted by residual: angle pdb=" N TYR G 95 " pdb=" CA TYR G 95 " pdb=" C TYR G 95 " ideal model delta sigma weight residual 107.57 113.41 -5.84 1.94e+00 2.66e-01 9.08e+00 angle pdb=" C TRP C 78 " pdb=" N ALA C 79 " pdb=" CA ALA C 79 " ideal model delta sigma weight residual 119.78 123.20 -3.42 1.24e+00 6.50e-01 7.60e+00 angle pdb=" N ILE H 30 " pdb=" CA ILE H 30 " pdb=" C ILE H 30 " ideal model delta sigma weight residual 112.98 110.27 2.71 1.25e+00 6.40e-01 4.70e+00 angle pdb=" N LEU G 92 " pdb=" CA LEU G 92 " pdb=" C LEU G 92 " ideal model delta sigma weight residual 108.13 111.78 -3.65 1.72e+00 3.38e-01 4.51e+00 angle pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 117.69 119.49 -1.80 9.30e-01 1.16e+00 3.75e+00 ... (remaining 13697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5483 17.82 - 35.64: 342 35.64 - 53.45: 76 53.45 - 71.27: 14 71.27 - 89.09: 11 Dihedral angle restraints: 5926 sinusoidal: 2246 harmonic: 3680 Sorted by residual: dihedral pdb=" CB GLU F 223 " pdb=" CG GLU F 223 " pdb=" CD GLU F 223 " pdb=" OE1 GLU F 223 " ideal model delta sinusoidal sigma weight residual 0.00 -89.09 89.09 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 24 " pdb=" CG GLU E 24 " pdb=" CD GLU E 24 " pdb=" OE1 GLU E 24 " ideal model delta sinusoidal sigma weight residual 0.00 87.10 -87.10 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA ASP D 28 " pdb=" CB ASP D 28 " pdb=" CG ASP D 28 " pdb=" OD1 ASP D 28 " ideal model delta sinusoidal sigma weight residual -30.00 -83.07 53.07 1 2.00e+01 2.50e-03 9.58e+00 ... (remaining 5923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 938 0.029 - 0.059: 374 0.059 - 0.088: 93 0.088 - 0.117: 103 0.117 - 0.147: 13 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA VAL F 115 " pdb=" N VAL F 115 " pdb=" C VAL F 115 " pdb=" CB VAL F 115 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA TYR G 95 " pdb=" N TYR G 95 " pdb=" C TYR G 95 " pdb=" CB TYR G 95 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE G 66 " pdb=" N ILE G 66 " pdb=" C ILE G 66 " pdb=" CB ILE G 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1518 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO H 14 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 15 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO H 16 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 16 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 16 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 95 " 0.012 2.00e-02 2.50e+03 7.24e-03 1.05e+00 pdb=" CG TYR G 95 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 95 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 95 " 0.004 2.00e-02 2.50e+03 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 594 2.72 - 3.26: 11004 3.26 - 3.81: 17721 3.81 - 4.35: 23220 4.35 - 4.90: 38368 Nonbonded interactions: 90907 Sorted by model distance: nonbonded pdb=" O SER H 75 " pdb=" OG SER H 76 " model vdw 2.173 2.440 nonbonded pdb=" OE1 GLN C 97 " pdb=" OH TYR A 93 " model vdw 2.211 2.440 nonbonded pdb=" O TRP K 92 " pdb=" NH1 ARG F 186 " model vdw 2.215 2.520 nonbonded pdb=" O ARG D 100 " pdb=" OG SER D 126 " model vdw 2.226 2.440 nonbonded pdb=" O TRP E 25 " pdb=" ND2 ASN E 31 " model vdw 2.233 2.520 ... (remaining 90902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.370 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: 2.470 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.610 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.002 0.033 10059 Z= 0.138 Angle : 0.433 5.845 13702 Z= 0.244 Chirality : 0.042 0.147 1521 Planarity : 0.002 0.050 1756 Dihedral : 12.959 89.090 3530 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.38 % Allowed : 7.22 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.19), residues: 1247 helix: -3.83 (0.22), residues: 213 sheet: -3.00 (0.21), residues: 411 loop : -2.91 (0.21), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS F 259 PHE 0.005 0.001 PHE G 185 TYR 0.016 0.001 TYR G 95 ARG 0.002 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASP cc_start: 0.6372 (t0) cc_final: 0.6155 (t0) REVERT: H 52 ASP cc_start: 0.7112 (t0) cc_final: 0.6618 (t0) REVERT: H 94 TYR cc_start: 0.7921 (m-80) cc_final: 0.7644 (m-80) REVERT: H 108 TYR cc_start: 0.8311 (m-80) cc_final: 0.7996 (m-80) REVERT: A 84 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5960 (mm-30) REVERT: A 103 VAL cc_start: 0.6957 (m) cc_final: 0.6527 (m) REVERT: B 87 ASP cc_start: 0.6558 (m-30) cc_final: 0.6157 (m-30) REVERT: D 58 VAL cc_start: 0.8789 (m) cc_final: 0.8539 (p) REVERT: D 86 LEU cc_start: 0.8372 (tp) cc_final: 0.8160 (tp) REVERT: D 91 TYR cc_start: 0.8332 (t80) cc_final: 0.8111 (t80) REVERT: E 58 VAL cc_start: 0.8072 (m) cc_final: 0.7860 (p) REVERT: E 83 LYS cc_start: 0.8191 (tptp) cc_final: 0.7441 (tptm) REVERT: G 20 ASP cc_start: 0.6930 (p0) cc_final: 0.6711 (p0) REVERT: G 227 MET cc_start: 0.7469 (tpp) cc_final: 0.7224 (tpp) REVERT: G 233 ARG cc_start: 0.7224 (mtm180) cc_final: 0.6753 (mtm-85) REVERT: F 34 LEU cc_start: 0.5580 (mt) cc_final: 0.4987 (mt) outliers start: 4 outliers final: 3 residues processed: 424 average time/residue: 0.2210 time to fit residues: 128.3762 Evaluate side-chains 300 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 297 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 GLN K 42 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS A 61 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN D 88 GLN E 88 GLN E 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** F 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10059 Z= 0.453 Angle : 0.741 6.941 13702 Z= 0.395 Chirality : 0.050 0.253 1521 Planarity : 0.006 0.115 1756 Dihedral : 4.930 21.671 1381 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.22 % Allowed : 17.45 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.22), residues: 1247 helix: -1.51 (0.31), residues: 215 sheet: -2.30 (0.22), residues: 420 loop : -2.00 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 108 HIS 0.016 0.002 HIS F 160 PHE 0.026 0.003 PHE F 156 TYR 0.019 0.002 TYR A 52 ARG 0.013 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 324 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASP cc_start: 0.6515 (t0) cc_final: 0.6288 (t0) REVERT: A 33 TYR cc_start: 0.8513 (p90) cc_final: 0.8146 (p90) REVERT: B 34 TYR cc_start: 0.8017 (m-80) cc_final: 0.7794 (m-80) REVERT: B 83 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7631 (tptp) REVERT: B 87 ASP cc_start: 0.8015 (m-30) cc_final: 0.7566 (m-30) REVERT: B 101 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8805 (pt) REVERT: D 88 GLN cc_start: 0.8268 (tp40) cc_final: 0.7964 (tp-100) REVERT: D 91 TYR cc_start: 0.8544 (t80) cc_final: 0.7838 (t80) REVERT: E 41 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7554 (mt-10) REVERT: F 91 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7458 (p0) REVERT: F 93 TYR cc_start: 0.7860 (m-80) cc_final: 0.7614 (m-80) outliers start: 45 outliers final: 21 residues processed: 341 average time/residue: 0.2203 time to fit residues: 103.3992 Evaluate side-chains 291 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 268 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN K 42 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN A 61 ASN A 97 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10059 Z= 0.233 Angle : 0.624 8.781 13702 Z= 0.327 Chirality : 0.047 0.196 1521 Planarity : 0.005 0.068 1756 Dihedral : 4.508 20.577 1378 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.56 % Allowed : 21.48 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.23), residues: 1247 helix: -0.48 (0.35), residues: 217 sheet: -1.92 (0.23), residues: 405 loop : -1.52 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 108 HIS 0.008 0.001 HIS F 259 PHE 0.022 0.002 PHE B 117 TYR 0.028 0.001 TYR D 33 ARG 0.017 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 307 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 69 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8177 (mtmm) REVERT: C 91 TYR cc_start: 0.8246 (t80) cc_final: 0.7909 (t80) REVERT: H 31 ASP cc_start: 0.6330 (t0) cc_final: 0.6097 (t0) REVERT: A 33 TYR cc_start: 0.8454 (p90) cc_final: 0.8147 (p90) REVERT: B 83 LYS cc_start: 0.8436 (tmtt) cc_final: 0.7647 (tptp) REVERT: B 87 ASP cc_start: 0.7959 (m-30) cc_final: 0.7496 (m-30) REVERT: D 91 TYR cc_start: 0.8305 (t80) cc_final: 0.7682 (t80) REVERT: E 41 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7418 (mt-10) REVERT: E 83 LYS cc_start: 0.8901 (tppt) cc_final: 0.8265 (tppt) REVERT: E 87 ASP cc_start: 0.7544 (m-30) cc_final: 0.7089 (m-30) REVERT: E 88 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: G 227 MET cc_start: 0.8659 (tpp) cc_final: 0.8345 (tpp) REVERT: F 27 TYR cc_start: 0.8329 (m-80) cc_final: 0.8024 (m-80) REVERT: F 91 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7033 (p0) REVERT: F 157 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8898 (mt) REVERT: F 204 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7015 (mt-10) outliers start: 38 outliers final: 23 residues processed: 331 average time/residue: 0.1981 time to fit residues: 92.2335 Evaluate side-chains 290 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 97 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 115 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 10059 Z= 0.596 Angle : 0.779 9.345 13702 Z= 0.409 Chirality : 0.052 0.273 1521 Planarity : 0.006 0.061 1756 Dihedral : 5.133 23.073 1378 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.53 % Allowed : 20.54 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.22), residues: 1247 helix: -0.89 (0.32), residues: 229 sheet: -1.75 (0.23), residues: 404 loop : -1.62 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 78 HIS 0.015 0.002 HIS F 259 PHE 0.022 0.003 PHE F 156 TYR 0.018 0.002 TYR E 93 ARG 0.017 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 273 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7867 (tp) REVERT: C 36 ASP cc_start: 0.7763 (t0) cc_final: 0.7538 (t0) REVERT: H 38 MET cc_start: 0.7334 (ttt) cc_final: 0.6307 (mtp) REVERT: H 61 ASN cc_start: 0.7917 (t0) cc_final: 0.7547 (t0) REVERT: H 80 HIS cc_start: 0.8255 (m-70) cc_final: 0.7992 (m90) REVERT: H 108 TYR cc_start: 0.7933 (m-80) cc_final: 0.7657 (m-80) REVERT: A 33 TYR cc_start: 0.8685 (p90) cc_final: 0.7953 (p90) REVERT: B 28 ASP cc_start: 0.7683 (m-30) cc_final: 0.7284 (m-30) REVERT: B 83 LYS cc_start: 0.8524 (tmtt) cc_final: 0.7546 (tptp) REVERT: B 87 ASP cc_start: 0.8208 (m-30) cc_final: 0.7643 (m-30) REVERT: D 24 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7816 (tm-30) REVERT: E 41 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 84 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7949 (mm-30) REVERT: E 88 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: G 202 PRO cc_start: 0.9168 (Cg_exo) cc_final: 0.8932 (Cg_endo) REVERT: F 27 TYR cc_start: 0.8451 (m-80) cc_final: 0.8245 (m-80) REVERT: F 157 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8972 (mt) REVERT: F 185 MET cc_start: 0.8532 (mpp) cc_final: 0.7902 (mpp) REVERT: F 211 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6347 (t-90) outliers start: 59 outliers final: 39 residues processed: 304 average time/residue: 0.1991 time to fit residues: 85.0558 Evaluate side-chains 291 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 211 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN C 115 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10059 Z= 0.228 Angle : 0.665 15.915 13702 Z= 0.341 Chirality : 0.049 0.305 1521 Planarity : 0.004 0.050 1756 Dihedral : 4.662 18.823 1378 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.41 % Allowed : 22.23 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.23), residues: 1247 helix: -0.35 (0.35), residues: 223 sheet: -1.57 (0.24), residues: 413 loop : -1.39 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 78 HIS 0.009 0.001 HIS F 160 PHE 0.012 0.002 PHE K 98 TYR 0.024 0.002 TYR E 33 ARG 0.013 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 288 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7658 (mm-30) REVERT: C 90 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7708 (ttm110) REVERT: H 4 LEU cc_start: 0.8679 (mm) cc_final: 0.8140 (mm) REVERT: H 80 HIS cc_start: 0.8032 (m-70) cc_final: 0.7700 (m90) REVERT: H 107 ASP cc_start: 0.7569 (t0) cc_final: 0.7264 (t0) REVERT: A 33 TYR cc_start: 0.8477 (p90) cc_final: 0.7997 (p90) REVERT: B 28 ASP cc_start: 0.7705 (m-30) cc_final: 0.7329 (m-30) REVERT: B 83 LYS cc_start: 0.8351 (tmtt) cc_final: 0.7648 (tptp) REVERT: B 87 ASP cc_start: 0.8233 (m-30) cc_final: 0.7780 (m-30) REVERT: D 91 TYR cc_start: 0.8449 (t80) cc_final: 0.8139 (t80) REVERT: E 83 LYS cc_start: 0.8917 (tppt) cc_final: 0.8465 (tppt) REVERT: E 88 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: G 112 TYR cc_start: 0.8103 (t80) cc_final: 0.7872 (t80) REVERT: G 202 PRO cc_start: 0.9115 (Cg_exo) cc_final: 0.8881 (Cg_endo) REVERT: F 157 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8655 (mt) REVERT: F 185 MET cc_start: 0.8463 (mpp) cc_final: 0.7933 (mpp) REVERT: F 204 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6322 (mt-10) outliers start: 47 outliers final: 30 residues processed: 315 average time/residue: 0.2108 time to fit residues: 92.5281 Evaluate side-chains 293 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 261 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 31 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10059 Z= 0.323 Angle : 0.689 13.330 13702 Z= 0.355 Chirality : 0.049 0.305 1521 Planarity : 0.004 0.048 1756 Dihedral : 4.682 19.690 1378 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.22 % Allowed : 22.89 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.23), residues: 1247 helix: -0.21 (0.34), residues: 237 sheet: -1.39 (0.24), residues: 407 loop : -1.25 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 78 HIS 0.009 0.001 HIS F 259 PHE 0.019 0.002 PHE F 156 TYR 0.017 0.002 TYR C 33 ARG 0.012 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ASP cc_start: 0.7334 (t0) cc_final: 0.7119 (t0) REVERT: C 37 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7605 (mm-30) REVERT: C 83 LYS cc_start: 0.8292 (tmmt) cc_final: 0.7391 (ttpp) REVERT: C 90 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7675 (ttm110) REVERT: H 4 LEU cc_start: 0.8574 (mm) cc_final: 0.8168 (mm) REVERT: H 80 HIS cc_start: 0.7890 (m-70) cc_final: 0.7626 (m90) REVERT: H 113 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (p) REVERT: A 33 TYR cc_start: 0.8528 (p90) cc_final: 0.7963 (p90) REVERT: A 112 LEU cc_start: 0.8620 (mp) cc_final: 0.8394 (mp) REVERT: B 28 ASP cc_start: 0.7778 (m-30) cc_final: 0.7448 (m-30) REVERT: B 87 ASP cc_start: 0.8192 (m-30) cc_final: 0.7990 (m-30) REVERT: E 88 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: E 93 TYR cc_start: 0.8654 (t80) cc_final: 0.8432 (t80) REVERT: G 202 PRO cc_start: 0.9108 (Cg_exo) cc_final: 0.8879 (Cg_endo) REVERT: F 157 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8898 (mt) REVERT: F 185 MET cc_start: 0.8479 (mpp) cc_final: 0.7907 (mpp) REVERT: F 204 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6847 (mt-10) REVERT: F 208 MET cc_start: 0.5983 (mmm) cc_final: 0.5476 (mmm) outliers start: 45 outliers final: 34 residues processed: 299 average time/residue: 0.1956 time to fit residues: 82.9022 Evaluate side-chains 293 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.7805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10059 Z= 0.350 Angle : 0.701 12.464 13702 Z= 0.362 Chirality : 0.048 0.294 1521 Planarity : 0.005 0.047 1756 Dihedral : 4.803 19.710 1378 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.60 % Allowed : 23.92 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.24), residues: 1247 helix: -0.22 (0.34), residues: 236 sheet: -1.35 (0.24), residues: 413 loop : -1.10 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 78 HIS 0.010 0.001 HIS F 259 PHE 0.026 0.002 PHE H 33 TYR 0.019 0.002 TYR H 27 ARG 0.011 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 270 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7642 (tp) REVERT: K 49 SER cc_start: 0.8596 (t) cc_final: 0.8379 (t) REVERT: C 37 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 90 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7650 (ttm110) REVERT: H 4 LEU cc_start: 0.8619 (mm) cc_final: 0.8275 (mm) REVERT: H 52 ASP cc_start: 0.7819 (t0) cc_final: 0.7317 (t0) REVERT: H 69 THR cc_start: 0.8563 (p) cc_final: 0.7605 (p) REVERT: H 80 HIS cc_start: 0.7990 (m-70) cc_final: 0.7781 (m90) REVERT: A 33 TYR cc_start: 0.8561 (p90) cc_final: 0.7878 (p90) REVERT: B 28 ASP cc_start: 0.7577 (m-30) cc_final: 0.7292 (m-30) REVERT: B 83 LYS cc_start: 0.8511 (tmtt) cc_final: 0.7755 (tptp) REVERT: B 86 LEU cc_start: 0.9172 (tp) cc_final: 0.8958 (tp) REVERT: B 87 ASP cc_start: 0.8221 (m-30) cc_final: 0.7718 (m-30) REVERT: D 24 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 88 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: G 202 PRO cc_start: 0.9118 (Cg_exo) cc_final: 0.8895 (Cg_endo) REVERT: F 157 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8921 (mt) REVERT: F 185 MET cc_start: 0.8522 (mpp) cc_final: 0.7968 (mpp) REVERT: F 248 GLU cc_start: 0.6875 (pm20) cc_final: 0.6667 (mp0) outliers start: 49 outliers final: 37 residues processed: 303 average time/residue: 0.1989 time to fit residues: 85.3252 Evaluate side-chains 298 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 258 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 0.0050 chunk 106 optimal weight: 7.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.8009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10059 Z= 0.378 Angle : 0.735 11.436 13702 Z= 0.377 Chirality : 0.049 0.290 1521 Planarity : 0.004 0.047 1756 Dihedral : 4.910 21.415 1378 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.69 % Allowed : 24.39 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.23), residues: 1247 helix: -0.57 (0.33), residues: 249 sheet: -1.36 (0.24), residues: 417 loop : -1.08 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 78 HIS 0.010 0.001 HIS F 259 PHE 0.047 0.002 PHE A 53 TYR 0.020 0.002 TYR H 27 ARG 0.015 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8355 (t) cc_final: 0.8101 (t) REVERT: C 33 TYR cc_start: 0.8131 (p90) cc_final: 0.7897 (p90) REVERT: C 36 ASP cc_start: 0.7176 (t0) cc_final: 0.6923 (t0) REVERT: C 37 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7607 (mm-30) REVERT: C 90 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7824 (ttm110) REVERT: C 108 TRP cc_start: 0.7828 (m100) cc_final: 0.7431 (m100) REVERT: C 123 VAL cc_start: 0.8618 (m) cc_final: 0.8366 (t) REVERT: H 4 LEU cc_start: 0.8451 (mm) cc_final: 0.8201 (mm) REVERT: H 19 LYS cc_start: 0.8041 (tppt) cc_final: 0.7705 (tppt) REVERT: H 38 MET cc_start: 0.7389 (tpp) cc_final: 0.6821 (mmt) REVERT: H 52 ASP cc_start: 0.7884 (t0) cc_final: 0.7229 (t0) REVERT: H 61 ASN cc_start: 0.6797 (t0) cc_final: 0.6276 (t0) REVERT: A 33 TYR cc_start: 0.8559 (p90) cc_final: 0.7844 (p90) REVERT: B 28 ASP cc_start: 0.7620 (m-30) cc_final: 0.7307 (m-30) REVERT: B 83 LYS cc_start: 0.8469 (tmtt) cc_final: 0.7795 (tptp) REVERT: B 87 ASP cc_start: 0.8233 (m-30) cc_final: 0.7736 (m-30) REVERT: D 24 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7836 (tm-30) REVERT: E 88 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: G 202 PRO cc_start: 0.9072 (Cg_exo) cc_final: 0.8857 (Cg_endo) REVERT: F 157 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8934 (mt) REVERT: F 185 MET cc_start: 0.8525 (mpp) cc_final: 0.7977 (mpp) REVERT: F 213 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7646 (mm-30) REVERT: F 248 GLU cc_start: 0.6928 (pm20) cc_final: 0.6605 (mp0) outliers start: 50 outliers final: 35 residues processed: 297 average time/residue: 0.2067 time to fit residues: 86.6008 Evaluate side-chains 289 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 252 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 0.0270 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN H 80 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10059 Z= 0.240 Angle : 0.697 13.349 13702 Z= 0.357 Chirality : 0.047 0.275 1521 Planarity : 0.004 0.047 1756 Dihedral : 4.752 21.565 1378 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.10 % Allowed : 26.27 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1247 helix: -0.36 (0.34), residues: 242 sheet: -1.02 (0.24), residues: 411 loop : -0.97 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 78 HIS 0.007 0.001 HIS F 259 PHE 0.036 0.002 PHE A 53 TYR 0.022 0.001 TYR H 27 ARG 0.012 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 277 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ASP cc_start: 0.7435 (t0) cc_final: 0.7226 (t0) REVERT: C 37 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7421 (mm-30) REVERT: C 90 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7689 (ttm110) REVERT: H 34 MET cc_start: 0.7514 (tpt) cc_final: 0.7270 (tpt) REVERT: H 38 MET cc_start: 0.7597 (tpp) cc_final: 0.6942 (mmm) REVERT: H 80 HIS cc_start: 0.7776 (m-70) cc_final: 0.7243 (m90) REVERT: H 94 TYR cc_start: 0.8095 (m-80) cc_final: 0.7865 (m-10) REVERT: H 106 MET cc_start: 0.8311 (mmm) cc_final: 0.8070 (mmm) REVERT: A 33 TYR cc_start: 0.8427 (p90) cc_final: 0.7837 (p90) REVERT: B 28 ASP cc_start: 0.7529 (m-30) cc_final: 0.7273 (m-30) REVERT: B 83 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8114 (tptp) REVERT: B 87 ASP cc_start: 0.8149 (m-30) cc_final: 0.7866 (m-30) REVERT: D 84 GLU cc_start: 0.7293 (mp0) cc_final: 0.7064 (mp0) REVERT: D 91 TYR cc_start: 0.8485 (t80) cc_final: 0.8270 (t80) REVERT: E 84 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7439 (mm-30) REVERT: E 88 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: G 202 PRO cc_start: 0.9034 (Cg_exo) cc_final: 0.8796 (Cg_endo) REVERT: F 157 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8807 (mt) REVERT: F 185 MET cc_start: 0.8495 (mpp) cc_final: 0.8022 (mpp) REVERT: F 210 GLU cc_start: 0.6749 (pm20) cc_final: 0.6113 (pm20) outliers start: 33 outliers final: 24 residues processed: 301 average time/residue: 0.1971 time to fit residues: 84.0504 Evaluate side-chains 282 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 10059 Z= 0.438 Angle : 0.766 12.749 13702 Z= 0.396 Chirality : 0.050 0.297 1521 Planarity : 0.006 0.084 1756 Dihedral : 5.185 24.810 1378 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.19 % Allowed : 26.27 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.24), residues: 1247 helix: -0.55 (0.33), residues: 243 sheet: -1.22 (0.24), residues: 417 loop : -0.97 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP E 78 HIS 0.011 0.001 HIS F 259 PHE 0.040 0.003 PHE A 53 TYR 0.036 0.002 TYR E 91 ARG 0.013 0.001 ARG H 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 257 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7670 (mm-30) REVERT: C 108 TRP cc_start: 0.7781 (m100) cc_final: 0.7360 (m100) REVERT: C 123 VAL cc_start: 0.8678 (m) cc_final: 0.8384 (t) REVERT: H 34 MET cc_start: 0.7321 (tpt) cc_final: 0.7057 (tpt) REVERT: H 36 TRP cc_start: 0.8837 (m100) cc_final: 0.7905 (m100) REVERT: H 38 MET cc_start: 0.7357 (tpp) cc_final: 0.6990 (mmm) REVERT: H 61 ASN cc_start: 0.6810 (t0) cc_final: 0.6310 (t0) REVERT: A 33 TYR cc_start: 0.8586 (p90) cc_final: 0.7837 (p90) REVERT: B 28 ASP cc_start: 0.7644 (m-30) cc_final: 0.7351 (m-30) REVERT: B 83 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8011 (tptp) REVERT: D 24 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7825 (tm-30) REVERT: E 84 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7844 (mm-30) REVERT: E 88 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: E 91 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7492 (t80) REVERT: G 124 GLU cc_start: 0.8345 (mm-30) cc_final: 0.6921 (mm-30) REVERT: G 128 MET cc_start: 0.8465 (mpp) cc_final: 0.7551 (mpp) REVERT: G 202 PRO cc_start: 0.9110 (Cg_exo) cc_final: 0.8892 (Cg_endo) REVERT: F 185 MET cc_start: 0.8510 (mpp) cc_final: 0.7988 (mpp) REVERT: F 210 GLU cc_start: 0.7375 (pm20) cc_final: 0.6851 (pm20) outliers start: 34 outliers final: 29 residues processed: 277 average time/residue: 0.2053 time to fit residues: 80.0636 Evaluate side-chains 277 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.0030 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 115 ASN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074268 restraints weight = 23955.241| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.30 r_work: 0.3328 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.8357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10059 Z= 0.264 Angle : 0.718 13.037 13702 Z= 0.371 Chirality : 0.048 0.279 1521 Planarity : 0.005 0.073 1756 Dihedral : 5.014 24.286 1378 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.81 % Allowed : 26.83 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.24), residues: 1247 helix: -0.48 (0.34), residues: 243 sheet: -1.19 (0.24), residues: 427 loop : -0.94 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 78 HIS 0.008 0.001 HIS F 259 PHE 0.041 0.002 PHE A 53 TYR 0.033 0.002 TYR E 91 ARG 0.011 0.001 ARG H 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.54 seconds wall clock time: 47 minutes 21.61 seconds (2841.61 seconds total)