Starting phenix.real_space_refine on Mon Aug 10 05:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zhq_74245/08_2026/9zhq_74245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zhq_74245/08_2026/9zhq_74245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zhq_74245/08_2026/9zhq_74245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zhq_74245/08_2026/9zhq_74245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zhq_74245/08_2026/9zhq_74245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zhq_74245/08_2026/9zhq_74245.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 240 5.16 5 C 12780 2.51 5 N 3852 2.21 5 O 4032 1.98 5 H 20448 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41352 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "D" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "E" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "F" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "G" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "H" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "I" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "J" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "K" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "M" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Chain: "N" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3446 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 220} Time building chain proxies: 6.68, per 1000 atoms: 0.16 Number of scatterers: 41352 At special positions: 0 Unit cell: (151.984, 151.158, 136.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 240 16.00 O 4032 8.00 N 3852 7.00 C 12780 6.00 H 20448 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=108, symmetry=0 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 111 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 181 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 57 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 59 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 63 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 181 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 57 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 59 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 120 " - pdb=" SG CYS E 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 32 " - pdb=" SG CYS F 57 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 59 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 60 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 120 " - pdb=" SG CYS F 156 " distance=2.03 Simple disulfide: pdb=" SG CYS F 181 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 57 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 59 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 60 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 111 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 120 " - pdb=" SG CYS G 156 " distance=2.03 Simple disulfide: pdb=" SG CYS G 181 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 57 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 60 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 71 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 81 " - pdb=" SG CYS H 111 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 120 " - pdb=" SG CYS H 156 " distance=2.03 Simple disulfide: pdb=" SG CYS H 181 " - pdb=" SG CYS H 248 " distance=2.03 Simple disulfide: pdb=" SG CYS I 32 " - pdb=" SG CYS I 57 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 59 " distance=2.03 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 60 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 63 " distance=2.03 Simple disulfide: pdb=" SG CYS I 71 " - pdb=" SG CYS I 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 81 " - pdb=" SG CYS I 111 " distance=2.03 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 120 " - pdb=" SG CYS I 156 " distance=2.03 Simple disulfide: pdb=" SG CYS I 181 " - pdb=" SG CYS I 248 " distance=2.03 Simple disulfide: pdb=" SG CYS J 32 " - pdb=" SG CYS J 57 " distance=2.03 Simple disulfide: pdb=" SG CYS J 35 " - pdb=" SG CYS J 59 " distance=2.03 Simple disulfide: pdb=" SG CYS J 40 " - pdb=" SG CYS J 60 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 63 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 87 " distance=2.03 Simple disulfide: pdb=" SG CYS J 81 " - pdb=" SG CYS J 111 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 120 " - pdb=" SG CYS J 156 " distance=2.03 Simple disulfide: pdb=" SG CYS J 181 " - pdb=" SG CYS J 248 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 57 " distance=2.03 Simple disulfide: pdb=" SG CYS K 35 " - pdb=" SG CYS K 59 " distance=2.03 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG CYS K 60 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 63 " distance=2.03 Simple disulfide: pdb=" SG CYS K 71 " - pdb=" SG CYS K 87 " distance=2.03 Simple disulfide: pdb=" SG CYS K 81 " - pdb=" SG CYS K 111 " distance=2.03 Simple disulfide: pdb=" SG CYS K 113 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 120 " - pdb=" SG CYS K 156 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 248 " distance=2.03 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 57 " distance=2.03 Simple disulfide: pdb=" SG CYS L 35 " - pdb=" SG CYS L 59 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 60 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 63 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 81 " - pdb=" SG CYS L 111 " distance=2.03 Simple disulfide: pdb=" SG CYS L 113 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 120 " - pdb=" SG CYS L 156 " distance=2.03 Simple disulfide: pdb=" SG CYS L 181 " - pdb=" SG CYS L 248 " distance=2.03 Simple disulfide: pdb=" SG CYS M 32 " - pdb=" SG CYS M 57 " distance=2.03 Simple disulfide: pdb=" SG CYS M 35 " - pdb=" SG CYS M 59 " distance=2.03 Simple disulfide: pdb=" SG CYS M 40 " - pdb=" SG CYS M 60 " distance=2.03 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 63 " distance=2.03 Simple disulfide: pdb=" SG CYS M 71 " - pdb=" SG CYS M 87 " distance=2.03 Simple disulfide: pdb=" SG CYS M 81 " - pdb=" SG CYS M 111 " distance=2.03 Simple disulfide: pdb=" SG CYS M 113 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 120 " - pdb=" SG CYS M 156 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 248 " distance=2.03 Simple disulfide: pdb=" SG CYS N 32 " - pdb=" SG CYS N 57 " distance=2.03 Simple disulfide: pdb=" SG CYS N 35 " - pdb=" SG CYS N 59 " distance=2.03 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 60 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 63 " distance=2.03 Simple disulfide: pdb=" SG CYS N 71 " - pdb=" SG CYS N 87 " distance=2.03 Simple disulfide: pdb=" SG CYS N 81 " - pdb=" SG CYS N 111 " distance=2.03 Simple disulfide: pdb=" SG CYS N 113 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 120 " - pdb=" SG CYS N 156 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4968 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 54 sheets defined 14.5% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 129 through 144 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'E' and resid 36 through 40 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 129 through 144 Processing helix chain 'E' and resid 239 through 243 Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 129 through 144 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 97 through 102 removed outlier: 3.661A pdb=" N ALA G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 102' Processing helix chain 'G' and resid 129 through 144 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 268 through 272 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 129 through 144 Processing helix chain 'H' and resid 239 through 243 Processing helix chain 'H' and resid 268 through 272 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 129 through 144 Processing helix chain 'I' and resid 239 through 243 Processing helix chain 'I' and resid 268 through 272 Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 129 through 144 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 268 through 272 Processing helix chain 'K' and resid 47 through 50 removed outlier: 4.405A pdb=" N LEU K 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 129 through 144 Processing helix chain 'K' and resid 239 through 243 Processing helix chain 'K' and resid 268 through 272 Processing helix chain 'L' and resid 36 through 40 Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 129 through 144 Processing helix chain 'L' and resid 239 through 243 Processing helix chain 'L' and resid 268 through 272 Processing helix chain 'M' and resid 74 through 78 Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 129 through 144 Processing helix chain 'M' and resid 239 through 243 Processing helix chain 'M' and resid 268 through 272 Processing helix chain 'N' and resid 36 through 40 Processing helix chain 'N' and resid 97 through 101 Processing helix chain 'N' and resid 129 through 144 Processing helix chain 'N' and resid 239 through 243 Processing helix chain 'N' and resid 268 through 272 Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 53 removed outlier: 4.111A pdb=" N MET C 62 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 88 Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'C' and resid 158 through 162 removed outlier: 4.876A pdb=" N GLY C 159 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE C 186 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 220 " --> pdb=" O THR N 220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE N 218 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR N 230 " --> pdb=" O ARG N 221 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU N 182 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE N 186 " --> pdb=" O GLY N 159 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLY N 159 " --> pdb=" O ILE N 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.583A pdb=" N ILE C 169 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL C 266 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN C 171 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 245 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 52 through 53 removed outlier: 4.105A pdb=" N MET D 62 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 88 Processing sheet with id=AA8, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 164 removed outlier: 6.771A pdb=" N ILE D 184 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 162 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU D 182 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR D 164 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER D 180 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 230 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 220 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER E 180 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR E 164 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLU E 182 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE E 162 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE E 184 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 172 removed outlier: 6.538A pdb=" N ILE D 169 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL D 266 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN D 171 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU D 245 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 88 Processing sheet with id=AB4, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.592A pdb=" N ILE E 169 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL E 266 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN E 171 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE E 263 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY E 244 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU E 245 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 251 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.844A pdb=" N MET F 62 " --> pdb=" O THR F 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 85 through 88 Processing sheet with id=AB8, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 162 removed outlier: 5.041A pdb=" N GLY F 159 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE F 186 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 230 " --> pdb=" O ARG G 221 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER G 180 " --> pdb=" O THR G 164 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR G 164 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU G 182 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE G 162 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE G 184 " --> pdb=" O PRO G 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.721A pdb=" N ILE F 169 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL F 266 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN F 171 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 244 " --> pdb=" O ILE F 263 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU F 245 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.848A pdb=" N MET G 62 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 85 through 88 Processing sheet with id=AC4, first strand: chain 'G' and resid 126 through 127 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 172 removed outlier: 6.604A pdb=" N ILE G 169 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL G 266 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN G 171 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU G 245 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 251 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AC7, first strand: chain 'H' and resid 85 through 88 Processing sheet with id=AC8, first strand: chain 'H' and resid 126 through 127 Processing sheet with id=AC9, first strand: chain 'H' and resid 158 through 164 removed outlier: 6.489A pdb=" N ILE H 184 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE H 162 " --> pdb=" O GLU H 182 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU H 182 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR H 164 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER H 180 " --> pdb=" O THR H 164 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 230 " --> pdb=" O ARG H 221 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE I 218 " --> pdb=" O GLY H 222 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR I 230 " --> pdb=" O ARG I 221 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER I 180 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR I 164 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU I 182 " --> pdb=" O ILE I 162 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE I 162 " --> pdb=" O GLU I 182 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE I 184 " --> pdb=" O PRO I 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 169 through 172 removed outlier: 6.568A pdb=" N ILE H 169 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL H 266 " --> pdb=" O ILE H 169 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN H 171 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU H 245 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 251 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 85 through 88 Processing sheet with id=AD3, first strand: chain 'I' and resid 119 through 121 removed outlier: 3.695A pdb=" N SER I 152 " --> pdb=" O CYS I 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 172 removed outlier: 6.697A pdb=" N ILE I 169 " --> pdb=" O THR I 264 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL I 266 " --> pdb=" O ILE I 169 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN I 171 " --> pdb=" O VAL I 266 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU I 245 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 52 through 53 removed outlier: 4.090A pdb=" N MET J 62 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 85 through 88 Processing sheet with id=AD7, first strand: chain 'J' and resid 126 through 127 removed outlier: 3.587A pdb=" N SER J 152 " --> pdb=" O CYS J 120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 158 through 164 removed outlier: 3.654A pdb=" N ILE J 186 " --> pdb=" O GLN J 158 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE J 184 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE J 162 " --> pdb=" O GLU J 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU J 182 " --> pdb=" O ILE J 162 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR J 164 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER J 180 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR J 230 " --> pdb=" O ARG J 221 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU K 182 " --> pdb=" O ILE K 162 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE K 162 " --> pdb=" O GLU K 182 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE K 184 " --> pdb=" O PRO K 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 169 through 172 removed outlier: 3.515A pdb=" N ASN J 171 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU J 245 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER J 251 " --> pdb=" O VAL J 190 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 52 through 53 removed outlier: 4.307A pdb=" N MET K 62 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR K 80 " --> pdb=" O CYS K 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 85 through 88 Processing sheet with id=AE3, first strand: chain 'K' and resid 126 through 127 Processing sheet with id=AE4, first strand: chain 'K' and resid 169 through 172 removed outlier: 6.611A pdb=" N ILE K 169 " --> pdb=" O THR K 264 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL K 266 " --> pdb=" O ILE K 169 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN K 171 " --> pdb=" O VAL K 266 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU K 245 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.585A pdb=" N MET L 62 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 85 through 88 Processing sheet with id=AE7, first strand: chain 'L' and resid 119 through 120 Processing sheet with id=AE8, first strand: chain 'L' and resid 158 through 164 removed outlier: 5.061A pdb=" N GLY L 159 " --> pdb=" O ILE L 186 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE L 186 " --> pdb=" O GLY L 159 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU L 182 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU M 182 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE M 186 " --> pdb=" O GLY M 159 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY M 159 " --> pdb=" O ILE M 186 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 169 through 172 removed outlier: 6.663A pdb=" N ILE L 169 " --> pdb=" O THR L 264 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL L 266 " --> pdb=" O ILE L 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN L 171 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER L 251 " --> pdb=" O VAL L 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 169 through 172 removed outlier: 6.663A pdb=" N ILE L 169 " --> pdb=" O THR L 264 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL L 266 " --> pdb=" O ILE L 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN L 171 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU L 245 " --> pdb=" O VAL L 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN L 194 " --> pdb=" O GLU L 247 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 52 through 53 removed outlier: 3.582A pdb=" N MET M 62 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 85 through 88 Processing sheet with id=AF4, first strand: chain 'M' and resid 126 through 127 Processing sheet with id=AF5, first strand: chain 'M' and resid 169 through 172 removed outlier: 6.693A pdb=" N ILE M 169 " --> pdb=" O THR M 264 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL M 266 " --> pdb=" O ILE M 169 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN M 171 " --> pdb=" O VAL M 266 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU M 245 " --> pdb=" O VAL M 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 52 through 53 removed outlier: 3.730A pdb=" N MET N 62 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR N 80 " --> pdb=" O CYS N 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 85 through 88 Processing sheet with id=AF8, first strand: chain 'N' and resid 126 through 127 Processing sheet with id=AF9, first strand: chain 'N' and resid 169 through 172 removed outlier: 6.595A pdb=" N ILE N 169 " --> pdb=" O THR N 264 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL N 266 " --> pdb=" O ILE N 169 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN N 171 " --> pdb=" O VAL N 266 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU N 245 " --> pdb=" O VAL N 196 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 1923 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: 11.25 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20448 1.03 - 1.23: 223 1.23 - 1.43: 8228 1.43 - 1.62: 12621 1.62 - 1.82: 264 Bond restraints: 41784 Sorted by residual: bond pdb=" C CYS N 60 " pdb=" N PRO N 61 " ideal model delta sigma weight residual 1.335 1.351 -0.016 8.70e-03 1.32e+04 3.43e+00 bond pdb=" C CYS D 60 " pdb=" N PRO D 61 " ideal model delta sigma weight residual 1.333 1.352 -0.018 1.01e-02 9.80e+03 3.28e+00 bond pdb=" C CYS K 60 " pdb=" N PRO K 61 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.01e-02 9.80e+03 3.04e+00 bond pdb=" C CYS C 60 " pdb=" N PRO C 61 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 2.81e+00 bond pdb=" C CYS I 60 " pdb=" N PRO I 61 " ideal model delta sigma weight residual 1.335 1.349 -0.014 8.70e-03 1.32e+04 2.62e+00 ... (remaining 41779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 70256 1.03 - 2.05: 5192 2.05 - 3.08: 368 3.08 - 4.11: 93 4.11 - 5.14: 15 Bond angle restraints: 75924 Sorted by residual: angle pdb=" N VAL L 151 " pdb=" CA VAL L 151 " pdb=" C VAL L 151 " ideal model delta sigma weight residual 113.10 109.43 3.67 9.70e-01 1.06e+00 1.43e+01 angle pdb=" N HIS E 227 " pdb=" CA HIS E 227 " pdb=" CB HIS E 227 " ideal model delta sigma weight residual 113.65 109.51 4.14 1.47e+00 4.63e-01 7.93e+00 angle pdb=" N HIS C 227 " pdb=" CA HIS C 227 " pdb=" CB HIS C 227 " ideal model delta sigma weight residual 113.65 109.59 4.06 1.47e+00 4.63e-01 7.64e+00 angle pdb=" N HIS G 227 " pdb=" CA HIS G 227 " pdb=" CB HIS G 227 " ideal model delta sigma weight residual 113.65 109.70 3.95 1.47e+00 4.63e-01 7.21e+00 angle pdb=" N ARG F 116 " pdb=" CA ARG F 116 " pdb=" C ARG F 116 " ideal model delta sigma weight residual 113.21 110.25 2.96 1.15e+00 7.56e-01 6.63e+00 ... (remaining 75919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 18018 17.38 - 34.76: 1271 34.76 - 52.14: 579 52.14 - 69.52: 189 69.52 - 86.90: 43 Dihedral angle restraints: 20100 sinusoidal: 11508 harmonic: 8592 Sorted by residual: dihedral pdb=" CA ASN N 194 " pdb=" C ASN N 194 " pdb=" N LYS N 195 " pdb=" CA LYS N 195 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA CYS K 59 " pdb=" C CYS K 59 " pdb=" N CYS K 60 " pdb=" CA CYS K 60 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG E 221 " pdb=" C ARG E 221 " pdb=" N GLY E 222 " pdb=" CA GLY E 222 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 20097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2090 0.030 - 0.060: 620 0.060 - 0.091: 151 0.091 - 0.121: 213 0.121 - 0.151: 34 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CA ILE C 272 " pdb=" N ILE C 272 " pdb=" C ILE C 272 " pdb=" CB ILE C 272 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE D 272 " pdb=" N ILE D 272 " pdb=" C ILE D 272 " pdb=" CB ILE D 272 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE F 272 " pdb=" N ILE F 272 " pdb=" C ILE F 272 " pdb=" CB ILE F 272 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 3105 not shown) Planarity restraints: 6540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 82 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO G 83 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 127 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO K 128 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO K 128 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 128 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 127 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO D 128 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.017 5.00e-02 4.00e+02 ... (remaining 6537 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 6661 2.27 - 2.85: 94846 2.85 - 3.43: 100851 3.43 - 4.02: 138246 4.02 - 4.60: 210343 Nonbonded interactions: 550947 Sorted by model distance: nonbonded pdb=" HE ARG F 221 " pdb="HE21 GLN G 219 " model vdw 1.685 2.100 nonbonded pdb=" HZ3 TRP F 232 " pdb="HE22 GLN G 219 " model vdw 1.834 2.100 nonbonded pdb=" H SER F 90 " pdb=" HA2 GLY F 109 " model vdw 1.903 2.270 nonbonded pdb=" H GLN G 176 " pdb=" HG3 GLN G 176 " model vdw 1.919 2.270 nonbonded pdb=" H SER K 90 " pdb=" HA2 GLY K 109 " model vdw 1.931 2.270 ... (remaining 550942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. 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: 3.850 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: 0.290 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.980 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21444 Z= 0.163 Angle : 0.597 5.136 29136 Z= 0.334 Chirality : 0.042 0.151 3108 Planarity : 0.004 0.032 3900 Dihedral : 10.241 86.899 8040 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.03 % Allowed : 5.56 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2880 helix: 2.71 (0.36), residues: 192 sheet: -0.37 (0.18), residues: 791 loop : 0.03 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.008 0.001 TYR N 80 TRP 0.011 0.001 TRP D 170 HIS 0.004 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (21336) covalent geometry : angle 0.59576 / 0.33 (28920) SS BOND : bond 0.00186 / 0.13 ( 108) SS BOND : angle 0.73347 / 0.52 ( 216) hydrogen bonds : bond 0.22958 / 16.02 ( 812) hydrogen bonds : angle 9.64282 / 6.82 ( 1923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 ILE cc_start: 0.8698 (pt) cc_final: 0.8162 (mm) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1080 time to fit residues: 2.5980 Evaluate side-chains 11 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.079734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.057203 restraints weight = 54754.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.059789 restraints weight = 25205.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.061445 restraints weight = 15310.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.062149 restraints weight = 11176.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.062454 restraints weight = 9505.818| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 1.0132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21444 Z= 0.184 Angle : 0.760 6.369 29136 Z= 0.421 Chirality : 0.045 0.156 3108 Planarity : 0.007 0.092 3900 Dihedral : 6.297 39.516 3132 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2880 helix: 2.33 (0.37), residues: 192 sheet: 1.01 (0.18), residues: 780 loop : 0.18 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 65 TYR 0.015 0.002 TYR I 127 TRP 0.023 0.003 TRP M 170 HIS 0.005 0.002 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (21336) covalent geometry : angle 0.75531 / 0.42 (28920) SS BOND : bond 0.00365 / 0.25 ( 108) SS BOND : angle 1.20036 / 0.81 ( 216) hydrogen bonds : bond 0.07637 / 5.42 ( 812) hydrogen bonds : angle 6.85872 / 4.88 ( 1923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 ILE cc_start: 0.8482 (pt) cc_final: 0.8062 (mm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0768 time to fit residues: 1.3995 Evaluate side-chains 9 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 0.0270 chunk 248 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 21 optimal weight: 0.0270 chunk 257 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.083912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.058288 restraints weight = 56771.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.060558 restraints weight = 27184.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.062521 restraints weight = 17417.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.064110 restraints weight = 13504.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.064573 restraints weight = 10997.713| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 1.0190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21444 Z= 0.132 Angle : 0.608 4.842 29136 Z= 0.339 Chirality : 0.043 0.145 3108 Planarity : 0.006 0.080 3900 Dihedral : 5.510 20.821 3132 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2880 helix: 2.26 (0.36), residues: 192 sheet: 1.29 (0.17), residues: 816 loop : 0.19 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 221 TYR 0.006 0.001 TYR G 178 TRP 0.008 0.002 TRP K 232 HIS 0.002 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (21336) covalent geometry : angle 0.60697 / 0.34 (28920) SS BOND : bond 0.00490 / 0.33 ( 108) SS BOND : angle 0.75920 / 0.49 ( 216) hydrogen bonds : bond 0.06761 / 4.75 ( 812) hydrogen bonds : angle 6.36943 / 4.53 ( 1923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: -0.2069 (ttm) cc_final: -0.2761 (mtt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1237 time to fit residues: 2.4692 Evaluate side-chains 9 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 135 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 163 optimal weight: 0.0670 chunk 267 optimal weight: 50.0000 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.081910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.054756 restraints weight = 50670.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.057233 restraints weight = 25289.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.058821 restraints weight = 15545.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.059854 restraints weight = 11737.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.060332 restraints weight = 9967.825| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 1.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21444 Z= 0.146 Angle : 0.610 5.103 29136 Z= 0.340 Chirality : 0.042 0.147 3108 Planarity : 0.006 0.077 3900 Dihedral : 5.542 24.789 3132 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2880 helix: 2.27 (0.36), residues: 192 sheet: 1.54 (0.18), residues: 816 loop : 0.18 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 198 TYR 0.005 0.001 TYR F 178 TRP 0.003 0.001 TRP F 232 HIS 0.002 0.001 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (21336) covalent geometry : angle 0.60986 / 0.34 (28920) SS BOND : bond 0.00270 / 0.18 ( 108) SS BOND : angle 0.63141 / 0.43 ( 216) hydrogen bonds : bond 0.06307 / 4.47 ( 812) hydrogen bonds : angle 6.33889 / 4.49 ( 1923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0554 time to fit residues: 0.8409 Evaluate side-chains 9 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 0 optimal weight: 40.0000 chunk 209 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 chunk 29 optimal weight: 50.0000 chunk 24 optimal weight: 40.0000 chunk 190 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.083422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.057885 restraints weight = 56852.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.060319 restraints weight = 27063.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.062098 restraints weight = 17242.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062722 restraints weight = 13194.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.062912 restraints weight = 11550.238| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 1.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21444 Z= 0.134 Angle : 0.588 5.364 29136 Z= 0.324 Chirality : 0.043 0.147 3108 Planarity : 0.005 0.070 3900 Dihedral : 5.169 18.843 3132 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2880 helix: 2.42 (0.37), residues: 192 sheet: 1.48 (0.18), residues: 708 loop : 0.12 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 94 TYR 0.006 0.001 TYR F 178 TRP 0.004 0.001 TRP D 232 HIS 0.002 0.001 HIS I 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (21336) covalent geometry : angle 0.58760 / 0.32 (28920) SS BOND : bond 0.00361 / 0.24 ( 108) SS BOND : angle 0.67694 / 0.45 ( 216) hydrogen bonds : bond 0.06012 / 4.24 ( 812) hydrogen bonds : angle 6.08369 / 4.32 ( 1923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0546 time to fit residues: 0.8437 Evaluate side-chains 9 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 109 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 251 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 200 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 50.0000 chunk 193 optimal weight: 30.0000 chunk 258 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.083373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.057693 restraints weight = 57135.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060263 restraints weight = 26987.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.061950 restraints weight = 17023.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.062724 restraints weight = 13236.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.062898 restraints weight = 11529.905| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 1.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21444 Z= 0.108 Angle : 0.567 5.444 29136 Z= 0.309 Chirality : 0.043 0.146 3108 Planarity : 0.005 0.066 3900 Dihedral : 4.806 19.146 3132 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2880 helix: 2.56 (0.37), residues: 192 sheet: 1.60 (0.19), residues: 708 loop : 0.18 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 134 TYR 0.003 0.001 TYR M 80 TRP 0.007 0.001 TRP J 232 HIS 0.003 0.001 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (21336) covalent geometry : angle 0.56663 / 0.31 (28920) SS BOND : bond 0.00175 / 0.12 ( 108) SS BOND : angle 0.59983 / 0.39 ( 216) hydrogen bonds : bond 0.05659 / 3.98 ( 812) hydrogen bonds : angle 5.83803 / 4.13 ( 1923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0462 time to fit residues: 0.7126 Evaluate side-chains 9 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 70 optimal weight: 9.9990 chunk 26 optimal weight: 50.0000 chunk 209 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.083036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.056814 restraints weight = 59766.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.059074 restraints weight = 28394.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.060808 restraints weight = 18219.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.061457 restraints weight = 14175.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.061699 restraints weight = 12625.120| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 1.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21444 Z= 0.167 Angle : 0.583 5.734 29136 Z= 0.319 Chirality : 0.041 0.145 3108 Planarity : 0.005 0.061 3900 Dihedral : 4.734 19.336 3132 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2880 helix: 2.66 (0.37), residues: 192 sheet: 1.05 (0.19), residues: 708 loop : 0.26 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 221 TYR 0.005 0.001 TYR I 178 TRP 0.004 0.001 TRP F 193 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (21336) covalent geometry : angle 0.57987 / 0.32 (28920) SS BOND : bond 0.00222 / 0.15 ( 108) SS BOND : angle 0.91056 / 0.61 ( 216) hydrogen bonds : bond 0.05394 / 3.75 ( 812) hydrogen bonds : angle 5.89164 / 4.19 ( 1923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: D 62 MET cc_start: -0.2127 (ttm) cc_final: -0.2529 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0484 time to fit residues: 0.6406 Evaluate side-chains 6 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 150 optimal weight: 0.0370 chunk 108 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 211 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 246 optimal weight: 0.0170 chunk 143 optimal weight: 1.9990 chunk 169 optimal weight: 30.0000 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.083151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.057287 restraints weight = 54949.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.060110 restraints weight = 26007.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.061470 restraints weight = 16366.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062785 restraints weight = 12889.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.063189 restraints weight = 10911.771| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 1.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21444 Z= 0.108 Angle : 0.552 5.416 29136 Z= 0.301 Chirality : 0.043 0.143 3108 Planarity : 0.005 0.061 3900 Dihedral : 4.511 19.335 3132 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 2880 helix: 2.78 (0.38), residues: 192 sheet: 1.49 (0.19), residues: 708 loop : 0.35 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 205 TYR 0.004 0.001 TYR G 201 TRP 0.006 0.001 TRP N 232 HIS 0.001 0.000 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (21336) covalent geometry : angle 0.54976 / 0.30 (28920) SS BOND : bond 0.00204 / 0.14 ( 108) SS BOND : angle 0.77895 / 0.52 ( 216) hydrogen bonds : bond 0.05196 / 3.60 ( 812) hydrogen bonds : angle 5.76569 / 4.08 ( 1923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: D 62 MET cc_start: -0.3478 (ttm) cc_final: -0.3959 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0465 time to fit residues: 0.6291 Evaluate side-chains 6 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 256 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 chunk 159 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 72 optimal weight: 50.0000 chunk 187 optimal weight: 0.0170 chunk 62 optimal weight: 3.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.083163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.057461 restraints weight = 54914.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.060085 restraints weight = 25903.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.061767 restraints weight = 16476.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.062490 restraints weight = 12837.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.062706 restraints weight = 11187.649| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 1.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21444 Z= 0.106 Angle : 0.539 4.975 29136 Z= 0.294 Chirality : 0.043 0.147 3108 Planarity : 0.004 0.056 3900 Dihedral : 4.351 19.529 3132 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2880 helix: 3.02 (0.38), residues: 192 sheet: 1.69 (0.19), residues: 708 loop : 0.37 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 134 TYR 0.002 0.001 TYR F 246 TRP 0.006 0.001 TRP H 232 HIS 0.002 0.000 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (21336) covalent geometry : angle 0.53783 / 0.29 (28920) SS BOND : bond 0.00157 / 0.11 ( 108) SS BOND : angle 0.70772 / 0.47 ( 216) hydrogen bonds : bond 0.04906 / 3.37 ( 812) hydrogen bonds : angle 5.62146 / 3.97 ( 1923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.075 Fit side-chains REVERT: D 62 MET cc_start: -0.3199 (ttm) cc_final: -0.3634 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0471 time to fit residues: 0.6109 Evaluate side-chains 6 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 279 optimal weight: 0.0770 chunk 198 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 277 optimal weight: 0.1980 chunk 214 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 51 optimal weight: 30.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.082795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.056955 restraints weight = 58194.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.059274 restraints weight = 27494.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.060715 restraints weight = 17570.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.061199 restraints weight = 14041.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.062346 restraints weight = 12831.593| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 1.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21444 Z= 0.133 Angle : 0.560 5.314 29136 Z= 0.304 Chirality : 0.042 0.146 3108 Planarity : 0.004 0.056 3900 Dihedral : 4.380 18.931 3132 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2880 helix: 3.04 (0.37), residues: 192 sheet: 1.44 (0.19), residues: 708 loop : 0.36 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 134 TYR 0.003 0.001 TYR I 178 TRP 0.005 0.001 TRP H 170 HIS 0.003 0.001 HIS I 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (21336) covalent geometry : angle 0.55796 / 0.30 (28920) SS BOND : bond 0.00158 / 0.11 ( 108) SS BOND : angle 0.80468 / 0.58 ( 216) hydrogen bonds : bond 0.04861 / 3.33 ( 812) hydrogen bonds : angle 5.65881 / 4.01 ( 1923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.097 Fit side-chains REVERT: D 62 MET cc_start: -0.3305 (ttm) cc_final: -0.3771 (mtt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0422 time to fit residues: 0.5522 Evaluate side-chains 6 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 48 optimal weight: 50.0000 chunk 121 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 226 optimal weight: 30.0000 chunk 44 optimal weight: 0.2980 chunk 268 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 143 optimal weight: 0.6980 chunk 152 optimal weight: 0.0170 chunk 276 optimal weight: 2.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.083081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.056915 restraints weight = 59333.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.059452 restraints weight = 28031.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.061237 restraints weight = 17901.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.061871 restraints weight = 13956.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.062120 restraints weight = 12499.170| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 1.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21444 Z= 0.103 Angle : 0.535 5.189 29136 Z= 0.291 Chirality : 0.043 0.147 3108 Planarity : 0.004 0.055 3900 Dihedral : 4.237 18.791 3132 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.16), residues: 2880 helix: 2.79 (0.36), residues: 192 sheet: 1.59 (0.18), residues: 792 loop : 0.43 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 143 TYR 0.003 0.001 TYR N 80 TRP 0.007 0.001 TRP M 232 HIS 0.003 0.001 HIS I 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (21336) covalent geometry : angle 0.53471 / 0.29 (28920) SS BOND : bond 0.00190 / 0.14 ( 108) SS BOND : angle 0.62630 / 0.43 ( 216) hydrogen bonds : bond 0.04779 / 3.27 ( 812) hydrogen bonds : angle 5.58400 / 3.95 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.19 seconds wall clock time: 45 minutes 13.15 seconds (2713.15 seconds total)