Starting phenix.real_space_refine (version: dev) on Sun Feb 19 09:54:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/02_2023/6vx4_21429.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/02_2023/6vx4_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_21429/02_2023/6vx4_21429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/02_2023/6vx4_21429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/02_2023/6vx4_21429.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx4_21429/02_2023/6vx4_21429.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 5.65, per 1000 atoms: 0.58 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: 4.29 Conformation dependent library (CDL) restraints added in 1.4 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: 0.62 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: 3.03 Time building geometry restraints manager: 4.52 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 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. 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: 0.460 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: 2.930 Check model and map are aligned: 0.150 Process input model: 29.180 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 % 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 *********************** 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 : 1.245 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 outliers start: 4 outliers final: 3 residues processed: 424 average time/residue: 0.2289 time to fit residues: 132.5060 Evaluate side-chains 303 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 300 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1196 time to fit residues: 2.1631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 ASN C 97 GLN ** 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 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7997 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 10059 Z= 0.415 Angle : 0.719 6.943 13702 Z= 0.384 Chirality : 0.050 0.240 1521 Planarity : 0.006 0.120 1756 Dihedral : 4.733 21.372 1377 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 4.22 % 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: -3.13 (0.22), residues: 1247 helix: -1.54 (0.31), residues: 215 sheet: -2.31 (0.22), residues: 420 loop : -2.00 (0.24), residues: 612 *********************** 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 375 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 330 time to evaluate : 1.214 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 outliers start: 45 outliers final: 23 residues processed: 346 average time/residue: 0.2311 time to fit residues: 110.5275 Evaluate side-chains 292 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 269 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1152 time to fit residues: 6.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 ASN C 97 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN F 128 GLN ** F 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10059 Z= 0.228 Angle : 0.625 8.632 13702 Z= 0.329 Chirality : 0.047 0.213 1521 Planarity : 0.005 0.075 1756 Dihedral : 4.403 18.139 1377 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.23), residues: 1247 helix: -0.45 (0.35), residues: 212 sheet: -1.88 (0.23), residues: 413 loop : -1.46 (0.25), residues: 622 *********************** 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 331 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 319 average time/residue: 0.2237 time to fit residues: 99.3289 Evaluate side-chains 282 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 267 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1268 time to fit residues: 4.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 115 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 10059 Z= 0.466 Angle : 0.733 8.633 13702 Z= 0.382 Chirality : 0.051 0.260 1521 Planarity : 0.005 0.071 1756 Dihedral : 4.922 22.238 1377 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 25.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.23), residues: 1247 helix: -0.45 (0.34), residues: 218 sheet: -1.50 (0.24), residues: 397 loop : -1.47 (0.25), residues: 632 *********************** 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 323 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 283 time to evaluate : 1.284 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 outliers start: 40 outliers final: 18 residues processed: 304 average time/residue: 0.2271 time to fit residues: 95.8346 Evaluate side-chains 272 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0929 time to fit residues: 4.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 31 ASN C 115 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10059 Z= 0.289 Angle : 0.656 9.410 13702 Z= 0.341 Chirality : 0.048 0.255 1521 Planarity : 0.004 0.046 1756 Dihedral : 4.630 20.214 1377 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 1.59 % 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: -1.85 (0.23), residues: 1247 helix: -0.23 (0.34), residues: 222 sheet: -1.49 (0.23), residues: 413 loop : -1.31 (0.26), residues: 612 *********************** 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 291 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 274 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 282 average time/residue: 0.2193 time to fit residues: 86.6346 Evaluate side-chains 255 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 248 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0929 time to fit residues: 2.6433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 ASN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10059 Z= 0.315 Angle : 0.665 9.937 13702 Z= 0.345 Chirality : 0.047 0.195 1521 Planarity : 0.004 0.046 1756 Dihedral : 4.651 21.129 1377 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 2.25 % 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: -1.67 (0.24), residues: 1247 helix: -0.21 (0.35), residues: 217 sheet: -1.36 (0.23), residues: 426 loop : -1.13 (0.26), residues: 604 *********************** 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 280 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 267 average time/residue: 0.2147 time to fit residues: 80.7686 Evaluate side-chains 256 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1027 time to fit residues: 3.5614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 10059 Z= 0.259 Angle : 0.665 10.331 13702 Z= 0.343 Chirality : 0.047 0.187 1521 Planarity : 0.004 0.045 1756 Dihedral : 4.619 21.353 1377 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.22 % 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: -1.55 (0.24), residues: 1247 helix: -0.21 (0.34), residues: 222 sheet: -1.21 (0.24), residues: 424 loop : -1.09 (0.26), residues: 601 *********************** 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 276 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 263 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 270 average time/residue: 0.2297 time to fit residues: 86.3852 Evaluate side-chains 247 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0958 time to fit residues: 2.6668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN C 115 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10059 Z= 0.281 Angle : 0.680 10.299 13702 Z= 0.350 Chirality : 0.047 0.255 1521 Planarity : 0.004 0.045 1756 Dihedral : 4.670 24.538 1377 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 1.31 % 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: -1.48 (0.24), residues: 1247 helix: -0.19 (0.34), residues: 222 sheet: -1.20 (0.24), residues: 423 loop : -0.99 (0.26), residues: 602 *********************** 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 275 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 1.226 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 outliers start: 14 outliers final: 7 residues processed: 266 average time/residue: 0.2241 time to fit residues: 83.8174 Evaluate side-chains 247 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1014 time to fit residues: 2.8846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 10059 Z= 0.346 Angle : 0.718 10.664 13702 Z= 0.373 Chirality : 0.048 0.233 1521 Planarity : 0.005 0.074 1756 Dihedral : 4.930 27.442 1377 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.56 % 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: -1.51 (0.24), residues: 1247 helix: -0.38 (0.35), residues: 222 sheet: -1.14 (0.24), residues: 426 loop : -0.99 (0.27), residues: 599 *********************** 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 250 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 249 average time/residue: 0.2234 time to fit residues: 78.2601 Evaluate side-chains 236 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0969 time to fit residues: 2.0383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10059 Z= 0.246 Angle : 0.707 12.146 13702 Z= 0.363 Chirality : 0.047 0.213 1521 Planarity : 0.005 0.066 1756 Dihedral : 4.763 24.821 1377 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.00 % 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: -1.41 (0.24), residues: 1247 helix: -0.25 (0.35), residues: 221 sheet: -1.06 (0.25), residues: 417 loop : -0.98 (0.26), residues: 609 ********************** 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 257 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2278 time to fit residues: 81.6342 Evaluate side-chains 239 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 0.0170 chunk 40 optimal weight: 0.0570 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.089834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076644 restraints weight = 23874.702| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.29 r_work: 0.3357 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.8294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10059 Z= 0.226 Angle : 0.722 12.657 13702 Z= 0.374 Chirality : 0.047 0.181 1521 Planarity : 0.005 0.064 1756 Dihedral : 4.767 26.505 1377 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.35 (0.24), residues: 1247 helix: -0.24 (0.34), residues: 221 sheet: -1.00 (0.25), residues: 417 loop : -0.94 (0.26), residues: 609 =============================================================================== Job complete usr+sys time: 2587.47 seconds wall clock time: 48 minutes 12.21 seconds (2892.21 seconds total)