Starting phenix.real_space_refine (version: dev) on Wed Feb 22 00:34:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwk_26834/02_2023/7uwk_26834.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwk_26834/02_2023/7uwk_26834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwk_26834/02_2023/7uwk_26834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwk_26834/02_2023/7uwk_26834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwk_26834/02_2023/7uwk_26834.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwk_26834/02_2023/7uwk_26834.pdb" } resolution = 4.4 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= 0.009 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 "A GLU 148": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I GLU 195": "OE1" <-> "OE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16064 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1899 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1804 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1917 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 808 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1879 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 228} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 778 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1875 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 227} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1944 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 8.86, per 1000 atoms: 0.55 Number of scatterers: 16064 At special positions: 0 Unit cell: (214.704, 127.8, 144.84, 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 149 16.00 O 2945 8.00 N 2882 7.00 C 10088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 170 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 102 " distance=2.04 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 99 " distance=2.04 Simple disulfide: pdb=" SG CYS I 162 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 187 " - pdb=" SG CYS I 271 " distance=2.03 Simple disulfide: pdb=" SG CYS I 257 " - pdb=" SG CYS I 261 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 168 " distance=2.04 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 170 " distance=2.03 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 102 " distance=2.04 Simple disulfide: pdb=" SG CYS K 87 " - pdb=" SG CYS K 99 " distance=2.03 Simple disulfide: pdb=" SG CYS K 162 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 187 " - pdb=" SG CYS K 271 " distance=2.03 Simple disulfide: pdb=" SG CYS K 257 " - pdb=" SG CYS K 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 170 " distance=2.03 Simple disulfide: pdb=" SG CYS J 24 " - pdb=" SG CYS J 102 " distance=2.04 Simple disulfide: pdb=" SG CYS J 87 " - pdb=" SG CYS J 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J 162 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 187 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 257 " - pdb=" SG CYS J 261 " distance=2.03 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 168 " distance=2.04 Simple disulfide: pdb=" SG CYS H 115 " - pdb=" SG CYS H 170 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 102 " distance=2.03 Simple disulfide: pdb=" SG CYS L 87 " - pdb=" SG CYS L 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 162 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 187 " - pdb=" SG CYS L 271 " distance=2.03 Simple disulfide: pdb=" SG CYS L 257 " - pdb=" SG CYS L 261 " 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: 5.05 Conformation dependent library (CDL) restraints added in 2.0 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3844 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 50 sheets defined 4.8% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.661A pdb=" N MET C 35 " --> pdb=" O PRO C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.534A pdb=" N LEU C 80 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 removed outlier: 4.391A pdb=" N TYR C 169 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.928A pdb=" N CYS C 261 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 257 through 261 removed outlier: 4.028A pdb=" N CYS D 261 " --> pdb=" O GLY D 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'I' and resid 170 through 176 removed outlier: 3.613A pdb=" N ALA I 176 " --> pdb=" O LYS I 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 36 Processing helix chain 'K' and resid 170 through 175 Processing helix chain 'J' and resid 31 through 36 removed outlier: 3.685A pdb=" N MET J 35 " --> pdb=" O PRO J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 168 removed outlier: 3.702A pdb=" N LYS J 168 " --> pdb=" O HIS J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 176 Processing helix chain 'L' and resid 31 through 36 Processing helix chain 'L' and resid 76 through 80 removed outlier: 3.517A pdb=" N LEU L 80 " --> pdb=" O SER L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 96 removed outlier: 3.621A pdb=" N HIS A 107 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 141 removed outlier: 6.296A pdb=" N ASN A 129 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS A 170 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU A 131 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 168 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 133 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 158 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 26 removed outlier: 4.010A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN C 103 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 25 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 101 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS C 102 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 137 " --> pdb=" O CYS C 87 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C 153 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 54 removed outlier: 3.701A pdb=" N LEU C 65 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE C 64 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET C 66 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 125 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.575A pdb=" N VAL C 235 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 221 through 223 removed outlier: 3.762A pdb=" N VAL C 222 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR C 207 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 263 through 264 removed outlier: 6.573A pdb=" N ARG C 263 " --> pdb=" O MET B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.552A pdb=" N LEU B 105 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.840A pdb=" N GLU B 131 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 169 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.657A pdb=" N HIS B 135 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 164 " --> pdb=" O HIS B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 26 removed outlier: 4.244A pdb=" N GLY D 25 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 101 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 83 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS D 139 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 91 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL D 133 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.588A pdb=" N ASP D 47 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 53 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.588A pdb=" N ASP D 47 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE D 64 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET D 66 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP D 70 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE D 121 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 236 removed outlier: 7.013A pdb=" N ALA D 186 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 216 through 218 removed outlier: 3.640A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 251 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 96 removed outlier: 4.268A pdb=" N ARG E 91 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 109 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU E 93 " --> pdb=" O HIS E 107 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS E 107 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP E 95 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 105 " --> pdb=" O ASP E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 138 removed outlier: 3.883A pdb=" N ALA E 167 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS E 135 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER E 165 " --> pdb=" O HIS E 135 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN E 137 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG E 163 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AC3, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.806A pdb=" N GLY I 25 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 88 " --> pdb=" O SER I 98 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL I 100 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA I 83 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS I 85 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS I 139 " --> pdb=" O LYS I 85 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR I 89 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 135 " --> pdb=" O THR I 89 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL I 133 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 136 " --> pdb=" O VAL I 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 45 through 52 removed outlier: 3.550A pdb=" N ASP I 47 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR I 123 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP I 70 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE I 121 " --> pdb=" O TRP I 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 235 through 238 removed outlier: 3.525A pdb=" N VAL I 196 " --> pdb=" O VAL I 235 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 216 through 223 removed outlier: 4.409A pdb=" N GLY I 218 " --> pdb=" O ILE I 211 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE I 211 " --> pdb=" O GLY I 218 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER I 220 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA I 209 " --> pdb=" O SER I 220 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG I 206 " --> pdb=" O TYR I 253 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET I 208 " --> pdb=" O THR I 251 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR I 251 " --> pdb=" O MET I 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU I 250 " --> pdb=" O HIS I 264 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS I 264 " --> pdb=" O LEU I 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 93 removed outlier: 3.502A pdb=" N ARG G 109 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU G 93 " --> pdb=" O HIS G 107 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS G 107 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 129 through 131 removed outlier: 3.552A pdb=" N GLU G 131 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 169 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 136 removed outlier: 3.686A pdb=" N HIS G 135 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL G 164 " --> pdb=" O HIS G 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 139 through 141 removed outlier: 3.737A pdb=" N ARG G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 25 through 26 removed outlier: 4.191A pdb=" N GLY K 25 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG K 101 " --> pdb=" O GLY K 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'K' and resid 47 through 54 removed outlier: 3.516A pdb=" N TRP K 70 " --> pdb=" O PHE K 121 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE K 121 " --> pdb=" O TRP K 70 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.532A pdb=" N ALA K 83 " --> pdb=" O ILE K 141 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET K 153 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 235 through 238 removed outlier: 3.867A pdb=" N VAL K 269 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 206 through 207 removed outlier: 4.886A pdb=" N TYR K 207 " --> pdb=" O VAL K 222 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL K 222 " --> pdb=" O TYR K 207 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 210 through 212 removed outlier: 3.548A pdb=" N LEU K 210 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 92 through 96 removed outlier: 3.570A pdb=" N HIS F 107 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU F 105 " --> pdb=" O ASP F 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AE1, first strand: chain 'F' and resid 129 through 137 removed outlier: 3.879A pdb=" N ASN F 129 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA F 167 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS F 135 " --> pdb=" O SER F 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER F 165 " --> pdb=" O HIS F 135 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN F 137 " --> pdb=" O ARG F 163 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG F 163 " --> pdb=" O GLN F 137 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 175 through 176 Processing sheet with id=AE3, first strand: chain 'J' and resid 22 through 25 removed outlier: 4.648A pdb=" N GLY J 25 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG J 101 " --> pdb=" O GLY J 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 45 through 54 Processing sheet with id=AE5, first strand: chain 'J' and resid 95 through 96 removed outlier: 3.874A pdb=" N LYS J 91 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL J 133 " --> pdb=" O LYS J 91 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 187 through 188 Processing sheet with id=AE7, first strand: chain 'J' and resid 193 through 199 Processing sheet with id=AE8, first strand: chain 'J' and resid 216 through 223 removed outlier: 3.839A pdb=" N GLY J 218 " --> pdb=" O ILE J 211 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 129 through 137 removed outlier: 3.944A pdb=" N ALA H 167 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS H 135 " --> pdb=" O SER H 165 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER H 165 " --> pdb=" O HIS H 135 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN H 137 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG H 163 " --> pdb=" O GLN H 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 22 through 25 removed outlier: 3.690A pdb=" N GLN L 23 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN L 103 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY L 25 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG L 101 " --> pdb=" O GLY L 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 47 through 54 removed outlier: 3.828A pdb=" N ASP L 47 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP L 70 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE L 121 " --> pdb=" O TRP L 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 95 through 97 removed outlier: 3.522A pdb=" N SER L 96 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY L 90 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 136 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL L 155 " --> pdb=" O ILE L 136 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 235 through 238 removed outlier: 6.388A pdb=" N THR L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA L 186 " --> pdb=" O VAL L 269 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 216 through 223 removed outlier: 3.599A pdb=" N GLY L 218 " --> pdb=" O ILE L 211 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5288 1.35 - 1.47: 3878 1.47 - 1.59: 7076 1.59 - 1.71: 0 1.71 - 1.83: 197 Bond restraints: 16439 Sorted by residual: bond pdb=" C THR D 158 " pdb=" N SER D 159 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.46e-02 4.69e+03 1.63e+01 bond pdb=" C THR C 158 " pdb=" N SER C 159 " ideal model delta sigma weight residual 1.331 1.369 -0.038 2.07e-02 2.33e+03 3.43e+00 bond pdb=" CB PRO L 202 " pdb=" CG PRO L 202 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.85e+00 bond pdb=" C THR I 89 " pdb=" N GLY I 90 " ideal model delta sigma weight residual 1.332 1.322 0.010 6.60e-03 2.30e+04 2.42e+00 bond pdb=" CB PRO E 144 " pdb=" CG PRO E 144 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 ... (remaining 16434 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.31: 594 106.31 - 113.25: 8890 113.25 - 120.20: 5394 120.20 - 127.14: 7212 127.14 - 134.08: 215 Bond angle restraints: 22305 Sorted by residual: angle pdb=" C TYR D 253 " pdb=" N PHE D 254 " pdb=" CA PHE D 254 " ideal model delta sigma weight residual 120.51 111.96 8.55 1.45e+00 4.76e-01 3.48e+01 angle pdb=" C THR J 158 " pdb=" N SER J 159 " pdb=" CA SER J 159 " ideal model delta sigma weight residual 121.48 132.41 -10.93 2.04e+00 2.40e-01 2.87e+01 angle pdb=" C PRO D 252 " pdb=" N TYR D 253 " pdb=" CA TYR D 253 " ideal model delta sigma weight residual 123.04 115.49 7.55 1.59e+00 3.96e-01 2.26e+01 angle pdb=" N ASN H 83 " pdb=" CA ASN H 83 " pdb=" C ASN H 83 " ideal model delta sigma weight residual 113.17 107.98 5.19 1.26e+00 6.30e-01 1.70e+01 angle pdb=" C LYS K 91 " pdb=" N SER K 92 " pdb=" CA SER K 92 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 ... (remaining 22300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 8961 14.89 - 29.78: 792 29.78 - 44.66: 221 44.66 - 59.55: 30 59.55 - 74.44: 17 Dihedral angle restraints: 10021 sinusoidal: 4067 harmonic: 5954 Sorted by residual: dihedral pdb=" CB CYS K 87 " pdb=" SG CYS K 87 " pdb=" SG CYS K 99 " pdb=" CB CYS K 99 " ideal model delta sinusoidal sigma weight residual -86.00 -11.56 -74.44 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS J 87 " pdb=" SG CYS J 87 " pdb=" SG CYS J 99 " pdb=" CB CYS J 99 " ideal model delta sinusoidal sigma weight residual -86.00 -18.49 -67.51 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS I 187 " pdb=" SG CYS I 187 " pdb=" SG CYS I 271 " pdb=" CB CYS I 271 " ideal model delta sinusoidal sigma weight residual 93.00 159.25 -66.25 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 10018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1502 0.033 - 0.066: 594 0.066 - 0.098: 240 0.098 - 0.131: 129 0.131 - 0.164: 17 Chirality restraints: 2482 Sorted by residual: chirality pdb=" CG LEU H 101 " pdb=" CB LEU H 101 " pdb=" CD1 LEU H 101 " pdb=" CD2 LEU H 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CB ILE K 136 " pdb=" CA ILE K 136 " pdb=" CG1 ILE K 136 " pdb=" CG2 ILE K 136 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB VAL D 269 " pdb=" CA VAL D 269 " pdb=" CG1 VAL D 269 " pdb=" CG2 VAL D 269 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2479 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 201 " 0.074 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO L 202 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO L 202 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO L 202 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 143 " -0.059 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO E 144 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 201 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 202 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " -0.039 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 481 2.68 - 3.24: 15051 3.24 - 3.79: 23705 3.79 - 4.35: 30119 4.35 - 4.90: 47937 Nonbonded interactions: 117293 Sorted by model distance: nonbonded pdb=" NH1 ARG J 49 " pdb=" O VAL J 50 " model vdw 2.131 2.520 nonbonded pdb=" NH1 ARG C 49 " pdb=" O VAL C 50 " model vdw 2.134 2.520 nonbonded pdb=" OG1 THR C 112 " pdb=" O GLY C 117 " model vdw 2.139 2.440 nonbonded pdb=" NH1 ARG I 49 " pdb=" O VAL I 50 " model vdw 2.161 2.520 nonbonded pdb=" ND1 HIS H 114 " pdb=" O GLY H 128 " model vdw 2.168 2.520 ... (remaining 117288 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' and (resid 82 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 through 150 or (resid 151 through 152 a \ nd (name N or name CA or name C or name O or name CB )) or resid 153 through 177 \ )) selection = (chain 'B' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 150 or (resid 151 through 152 and \ (name N or name CA or name C or name O or name CB )) or resid 153 through 173 or \ (resid 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 177)) selection = (chain 'E' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 150 or (resid 151 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 173 or (resid 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 177)) selection = (chain 'F' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 151 or (resid 152 \ and (name N or name CA or name C or name O or name CB )) or resid 153 through 17 \ 3 or (resid 174 and (name N or name CA or name C or name O or name CB )) or resi \ d 175 through 177)) selection = (chain 'G' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 150 or (resid 151 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 173 or (resid 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 177)) selection = (chain 'H' and (resid 82 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 137 or (resid 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 150 or (resid 151 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 173 or (resid 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 177)) } ncs_group { reference = (chain 'C' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 53 or (resid 54 an \ d (name N or name CA or name C or name O or name CB )) or resid 55 through 74 or \ resid 77 through 142 or (resid 143 through 144 and (name N or name CA or name C \ or name O or name CB )) or resid 145 through 162 or (resid 163 and (name N or n \ ame CA or name C or name O or name CB )) or resid 164 through 188 or resid 194 t \ hrough 200 or resid 205 through 214 or (resid 215 through 217 and (name N or nam \ e CA or name C or name O or name CB )) or resid 218 through 224 or resid 227 thr \ ough 239 or resid 245 through 258 or (resid 259 and (name N or name CA or name C \ or name O or name CB )) or resid 260 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 270)) selection = (chain 'D' and (resid 19 through 52 or (resid 53 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 62 or (resid 63 and (na \ me N or name CA or name C or name O or name CB )) or resid 64 through 74 or resi \ d 77 through 117 or (resid 118 and (name N or name CA or name C or name O or nam \ e CB )) or resid 119 through 142 or (resid 143 through 144 and (name N or name C \ A or name C or name O or name CB )) or resid 145 through 148 or resid 151 throug \ h 214 or (resid 215 through 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 239 or resid 245 through 249 or (resid 250 and (na \ me N or name CA or name C or name O or name CB )) or resid 251 through 258 or (r \ esid 259 and (name N or name CA or name C or name O or name CB )) or resid 260 t \ hrough 269 or (resid 270 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'I' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 74 or resid 77 through 117 or (resid 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 148 or resid 151 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 188 or resid 194 through 200 or r \ esid 205 through 214 or (resid 215 through 217 and (name N or name CA or name C \ or name O or name CB )) or resid 218 through 224 or resid 227 through 239 or res \ id 245 through 249 or (resid 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 266 or (resid 267 and (name N or \ name CA or name C or name O or name CB )) or resid 268 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 148 or resid 151 through 162 or (resid 163 and (name N or nam \ e CA or name C or name O or name CB )) or resid 164 through 188 or resid 194 thr \ ough 200 or resid 205 through 214 or (resid 215 through 217 and (name N or name \ CA or name C or name O or name CB )) or resid 218 through 224 or resid 227 throu \ gh 239 or resid 245 through 249 or (resid 250 and (name N or name CA or name C o \ r name O or name CB )) or resid 251 through 258 or (resid 259 and (name N or nam \ e CA or name C or name O or name CB )) or resid 260 through 266 or (resid 267 an \ d (name N or name CA or name C or name O or name CB )) or resid 268 through 269 \ or (resid 270 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 74 or resid 77 through 117 or (resid 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 148 or resid 151 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 188 or resid 194 through 200 or r \ esid 205 through 239 or resid 245 through 249 or (resid 250 and (name N or name \ CA or name C or name O or name CB )) or resid 251 through 266 or (resid 267 and \ (name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or (resid 48 and (name N or \ name CA or name C or name O or name CB )) or resid 49 through 52 or (resid 53 th \ rough 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 62 or (resid 63 and (name N or name CA or name C or name O or name CB )) o \ r resid 64 through 74 or resid 77 through 117 or (resid 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 142 or (resid 143 thro \ ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 148 or resid 151 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 188 or resid 194 through 200 or r \ esid 205 through 214 or (resid 215 through 217 and (name N or name CA or name C \ or name O or name CB )) or resid 218 through 224 or resid 227 through 239 or res \ id 245 through 249 or (resid 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 266 or (resid 267 and (name N or \ name CA or name C or name O or name CB )) or resid 268 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB )))) } 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 149 5.16 5 C 10088 2.51 5 N 2882 2.21 5 O 2945 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.020 Extract box with map and model: 6.640 Check model and map are aligned: 0.250 Process input model: 39.190 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 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 : 0.004 0.084 16439 Z= 0.246 Angle : 0.801 10.932 22305 Z= 0.437 Chirality : 0.046 0.164 2482 Planarity : 0.007 0.109 2871 Dihedral : 12.348 72.433 6054 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.76 (0.18), residues: 2005 helix: -2.76 (0.58), residues: 64 sheet: -0.67 (0.19), residues: 744 loop : -1.41 (0.16), residues: 1197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 457 time to evaluate : 1.790 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: 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: 2 outliers final: 1 residues processed: 459 average time/residue: 0.3252 time to fit residues: 207.0110 Evaluate side-chains 412 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 411 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1407 time to fit residues: 2.7860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 95 optimal weight: 0.0870 chunk 117 optimal weight: 0.0970 chunk 182 optimal weight: 1.9990 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 152 HIS C 23 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN D 213 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS I 143 ASN G 83 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN K 212 GLN F 123 HIS F 152 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 GLN H 107 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16439 Z= 0.172 Angle : 0.613 10.164 22305 Z= 0.311 Chirality : 0.045 0.239 2482 Planarity : 0.005 0.069 2871 Dihedral : 5.215 25.352 2241 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.52 (0.18), residues: 2005 helix: -2.72 (0.58), residues: 60 sheet: -0.61 (0.19), residues: 723 loop : -1.16 (0.16), residues: 1222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 449 time to evaluate : 1.859 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: 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: 7 outliers final: 4 residues processed: 456 average time/residue: 0.3363 time to fit residues: 214.9129 Evaluate side-chains 419 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 415 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1355 time to fit residues: 3.4735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 182 optimal weight: 0.0870 chunk 197 optimal weight: 0.3980 chunk 162 optimal weight: 0.0000 chunk 181 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 23 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN G 123 HIS F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN J 212 GLN J 249 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16439 Z= 0.166 Angle : 0.608 9.426 22305 Z= 0.306 Chirality : 0.045 0.192 2482 Planarity : 0.005 0.063 2871 Dihedral : 5.014 25.175 2241 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.42 (0.18), residues: 2005 helix: -2.81 (0.55), residues: 66 sheet: -0.55 (0.18), residues: 794 loop : -1.07 (0.17), residues: 1145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 443 time to evaluate : 1.930 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: 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: 3 outliers final: 1 residues processed: 446 average time/residue: 0.3223 time to fit residues: 200.6308 Evaluate side-chains 406 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1575 time to fit residues: 3.0539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 0.0370 chunk 194 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 123 HIS ** K 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 16439 Z= 0.210 Angle : 0.626 10.593 22305 Z= 0.317 Chirality : 0.045 0.236 2482 Planarity : 0.005 0.069 2871 Dihedral : 5.068 24.997 2241 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.18), residues: 2005 helix: -2.83 (0.53), residues: 66 sheet: -0.65 (0.18), residues: 779 loop : -1.10 (0.17), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 444 time to evaluate : 1.699 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: 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: 3 outliers final: 1 residues processed: 447 average time/residue: 0.3332 time to fit residues: 208.2442 Evaluate side-chains 418 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1460 time to fit residues: 2.6149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 2.9990 chunk 110 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 80 optimal weight: 0.0770 chunk 165 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 174 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 111 GLN C 139 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN I 143 ASN ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN J 212 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 16439 Z= 0.163 Angle : 0.613 9.565 22305 Z= 0.306 Chirality : 0.044 0.253 2482 Planarity : 0.005 0.079 2871 Dihedral : 4.904 24.473 2241 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.39 (0.18), residues: 2005 helix: -2.64 (0.57), residues: 60 sheet: -0.58 (0.19), residues: 719 loop : -1.03 (0.17), residues: 1226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 1.837 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: 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: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.3279 time to fit residues: 208.1934 Evaluate side-chains 413 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 114 optimal weight: 0.0050 chunk 47 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 139 HIS G 83 ASN G 123 HIS F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 16439 Z= 0.230 Angle : 0.649 10.959 22305 Z= 0.328 Chirality : 0.045 0.211 2482 Planarity : 0.005 0.052 2871 Dihedral : 5.141 27.106 2241 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.46 (0.18), residues: 2005 helix: -2.34 (0.61), residues: 60 sheet: -0.67 (0.18), residues: 790 loop : -1.07 (0.18), residues: 1155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 1.849 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.3464 time to fit residues: 218.6946 Evaluate side-chains 415 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 163 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 119 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 16439 Z= 0.202 Angle : 0.637 10.035 22305 Z= 0.321 Chirality : 0.045 0.284 2482 Planarity : 0.005 0.048 2871 Dihedral : 5.123 26.071 2241 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.56 (0.18), residues: 2005 helix: -2.35 (0.61), residues: 60 sheet: -0.79 (0.18), residues: 808 loop : -1.10 (0.18), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 1.873 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: 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: 0 outliers final: 0 residues processed: 450 average time/residue: 0.3351 time to fit residues: 210.1786 Evaluate side-chains 412 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 16439 Z= 0.258 Angle : 0.688 11.778 22305 Z= 0.349 Chirality : 0.047 0.262 2482 Planarity : 0.005 0.058 2871 Dihedral : 5.445 27.016 2241 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.65 (0.18), residues: 2005 helix: -2.27 (0.62), residues: 60 sheet: -0.83 (0.19), residues: 762 loop : -1.19 (0.17), residues: 1183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 2.016 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: 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: 0 outliers final: 0 residues processed: 450 average time/residue: 0.3500 time to fit residues: 221.8671 Evaluate side-chains 415 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.2980 chunk 169 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 78 optimal weight: 0.0070 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.0040 chunk 163 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.3010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS C 23 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN H 137 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16439 Z= 0.174 Angle : 0.641 10.474 22305 Z= 0.319 Chirality : 0.045 0.237 2482 Planarity : 0.005 0.047 2871 Dihedral : 5.039 24.727 2241 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.47 (0.18), residues: 2005 helix: -2.24 (0.63), residues: 60 sheet: -0.76 (0.18), residues: 787 loop : -1.01 (0.18), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.827 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: 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: 0 outliers final: 0 residues processed: 445 average time/residue: 0.3245 time to fit residues: 202.7747 Evaluate side-chains 416 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 90 optimal weight: 0.0470 chunk 132 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 16439 Z= 0.275 Angle : 0.722 11.402 22305 Z= 0.363 Chirality : 0.047 0.228 2482 Planarity : 0.006 0.073 2871 Dihedral : 5.529 27.056 2241 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.18), residues: 2005 helix: -2.47 (0.64), residues: 60 sheet: -0.90 (0.19), residues: 759 loop : -1.23 (0.18), residues: 1186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 1.726 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: 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: 1 outliers final: 0 residues processed: 450 average time/residue: 0.3175 time to fit residues: 202.5555 Evaluate side-chains 413 residues out of total 1839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 HIS ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 HIS H 137 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** L 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.208650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.182263 restraints weight = 41958.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.184473 restraints weight = 51465.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.185730 restraints weight = 42651.009| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 16439 Z= 0.300 Angle : 0.738 12.354 22305 Z= 0.374 Chirality : 0.048 0.224 2482 Planarity : 0.006 0.055 2871 Dihedral : 5.770 28.002 2241 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.04 (0.18), residues: 2005 helix: -2.72 (0.56), residues: 72 sheet: -1.15 (0.19), residues: 748 loop : -1.38 (0.17), residues: 1185 =============================================================================== Job complete usr+sys time: 4115.49 seconds wall clock time: 74 minutes 50.08 seconds (4490.08 seconds total)