Starting phenix.real_space_refine on Mon Oct 26 02:56:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja0_61286/10_2026/9ja0_61286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja0_61286/10_2026/9ja0_61286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ja0_61286/10_2026/9ja0_61286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja0_61286/10_2026/9ja0_61286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ja0_61286/10_2026/9ja0_61286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja0_61286/10_2026/9ja0_61286.map" } resolution = 3.14 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12384 2.51 5 N 3492 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19716 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1643 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 202} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.42, per 1000 atoms: 0.12 Number of scatterers: 19716 At special positions: 0 Unit cell: (106.941, 116.889, 128.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3672 8.00 N 3492 7.00 C 12384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 45 " distance=1.96 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS C 14 " distance=2.04 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS E 45 " distance=2.01 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 45 " - pdb=" SG CYS D 14 " distance=2.01 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS F 14 " distance=2.00 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 45 " distance=2.00 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS L 45 " distance=2.01 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS H 14 " distance=2.01 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS I 14 " distance=2.00 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS I 45 " - pdb=" SG CYS J 14 " distance=2.01 Simple disulfide: pdb=" SG CYS I 198 " - pdb=" SG CYS I 218 " distance=2.03 Simple disulfide: pdb=" SG CYS J 45 " - pdb=" SG CYS K 14 " distance=2.01 Simple disulfide: pdb=" SG CYS J 198 " - pdb=" SG CYS J 218 " distance=2.03 Simple disulfide: pdb=" SG CYS K 45 " - pdb=" SG CYS L 14 " distance=2.01 Simple disulfide: pdb=" SG CYS K 198 " - pdb=" SG CYS K 218 " distance=2.03 Simple disulfide: pdb=" SG CYS L 198 " - pdb=" SG CYS L 218 " 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: 1.27 Conformation dependent library (CDL) restraints added in 864.6 milliseconds 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 67.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL B 27 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.511A pdb=" N ASP D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.659A pdb=" N GLU D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL E 27 " --> pdb=" O TRP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS E 131 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS F 131 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP F 152 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 175 Processing helix chain 'F' and resid 178 through 189 removed outlier: 3.659A pdb=" N GLU F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR F 216 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP G 152 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU G 187 " --> pdb=" O ASN G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL H 27 " --> pdb=" O TRP H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS H 131 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS H 140 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP H 152 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 189 removed outlier: 3.659A pdb=" N GLU H 187 " --> pdb=" O ASN H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 Processing helix chain 'H' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR H 216 " --> pdb=" O GLU H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL I 27 " --> pdb=" O TRP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS I 131 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS I 140 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 removed outlier: 3.511A pdb=" N ASP I 152 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 175 Processing helix chain 'I' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU I 187 " --> pdb=" O ASN I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 204 Processing helix chain 'I' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR I 216 " --> pdb=" O GLU I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL J 27 " --> pdb=" O TRP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 58 Processing helix chain 'J' and resid 62 through 84 removed outlier: 3.542A pdb=" N MET J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS J 131 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP J 152 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU J 187 " --> pdb=" O ASN J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 204 Processing helix chain 'J' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR J 216 " --> pdb=" O GLU J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL K 27 " --> pdb=" O TRP K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 120 Processing helix chain 'K' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS K 131 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 153 removed outlier: 3.511A pdb=" N ASP K 152 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 175 Processing helix chain 'K' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU K 187 " --> pdb=" O ASN K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR K 216 " --> pdb=" O GLU K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL L 27 " --> pdb=" O TRP L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 58 Processing helix chain 'L' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS L 131 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS L 140 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP L 152 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU L 187 " --> pdb=" O ASN L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 204 Processing helix chain 'L' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 4 Processing sheet with id=AB2, first strand: chain 'K' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'L' and resid 2 through 4 1128 hydrogen bonds defined for protein. 3348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6673 1.34 - 1.46: 3267 1.46 - 1.58: 9860 1.58 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 20088 Sorted by residual: bond pdb=" C ILE G 37 " pdb=" O ILE G 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.92e+00 bond pdb=" C ILE E 37 " pdb=" O ILE E 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.87e+00 bond pdb=" C ILE L 37 " pdb=" O ILE L 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.87e+00 bond pdb=" C ILE C 37 " pdb=" O ILE C 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.87e+00 bond pdb=" C ILE D 37 " pdb=" O ILE D 37 " ideal model delta sigma weight residual 1.242 1.228 0.014 8.60e-03 1.35e+04 2.74e+00 ... (remaining 20083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 26098 1.40 - 2.80: 972 2.80 - 4.20: 194 4.20 - 5.60: 36 5.60 - 7.01: 24 Bond angle restraints: 27324 Sorted by residual: angle pdb=" N PRO I 122 " pdb=" CA PRO I 122 " pdb=" C PRO I 122 " ideal model delta sigma weight residual 110.70 103.69 7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N PRO G 122 " pdb=" CA PRO G 122 " pdb=" C PRO G 122 " ideal model delta sigma weight residual 110.70 103.70 7.00 1.22e+00 6.72e-01 3.29e+01 angle pdb=" N PRO L 122 " pdb=" CA PRO L 122 " pdb=" C PRO L 122 " ideal model delta sigma weight residual 110.70 103.71 6.99 1.22e+00 6.72e-01 3.29e+01 angle pdb=" N PRO C 122 " pdb=" CA PRO C 122 " pdb=" C PRO C 122 " ideal model delta sigma weight residual 110.70 103.71 6.99 1.22e+00 6.72e-01 3.29e+01 angle pdb=" N PRO D 122 " pdb=" CA PRO D 122 " pdb=" C PRO D 122 " ideal model delta sigma weight residual 110.70 103.73 6.97 1.22e+00 6.72e-01 3.27e+01 ... (remaining 27319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.78: 11006 13.78 - 27.56: 994 27.56 - 41.34: 224 41.34 - 55.12: 88 55.12 - 68.90: 24 Dihedral angle restraints: 12336 sinusoidal: 4728 harmonic: 7608 Sorted by residual: dihedral pdb=" CG ARG F 143 " pdb=" CD ARG F 143 " pdb=" NE ARG F 143 " pdb=" CZ ARG F 143 " ideal model delta sinusoidal sigma weight residual 180.00 138.07 41.93 2 1.50e+01 4.44e-03 9.53e+00 dihedral pdb=" CG ARG C 143 " pdb=" CD ARG C 143 " pdb=" NE ARG C 143 " pdb=" CZ ARG C 143 " ideal model delta sinusoidal sigma weight residual 180.00 138.09 41.91 2 1.50e+01 4.44e-03 9.52e+00 dihedral pdb=" CG ARG E 143 " pdb=" CD ARG E 143 " pdb=" NE ARG E 143 " pdb=" CZ ARG E 143 " ideal model delta sinusoidal sigma weight residual 180.00 138.11 41.89 2 1.50e+01 4.44e-03 9.51e+00 ... (remaining 12333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2057 0.035 - 0.070: 805 0.070 - 0.105: 209 0.105 - 0.140: 61 0.140 - 0.174: 36 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 3165 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 48 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO G 49 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 48 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO C 49 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 48 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO J 49 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO J 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 49 " -0.027 5.00e-02 4.00e+02 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6476 2.84 - 3.35: 18623 3.35 - 3.87: 31246 3.87 - 4.38: 38257 4.38 - 4.90: 61702 Nonbonded interactions: 156304 Sorted by model distance: nonbonded pdb=" OG1 THR A 210 " pdb=" OE1 GLU C 71 " model vdw 2.319 3.040 nonbonded pdb=" OE1 GLU A 71 " pdb=" OG1 THR B 210 " model vdw 2.351 3.040 nonbonded pdb=" O SER H 44 " pdb=" OG SER H 44 " model vdw 2.366 3.040 nonbonded pdb=" O SER L 44 " pdb=" OG SER L 44 " model vdw 2.366 3.040 nonbonded pdb=" O SER I 44 " pdb=" OG SER I 44 " model vdw 2.366 3.040 ... (remaining 156299 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 15.520 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 0.070 20112 Z= 0.203 Angle : 0.669 7.005 27372 Z= 0.438 Chirality : 0.044 0.174 3168 Planarity : 0.006 0.049 3552 Dihedral : 11.921 68.899 7320 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.28 (0.12), residues: 2604 helix: -3.25 (0.08), residues: 1620 sheet: None (None), residues: 0 loop : -1.74 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 154 TYR 0.006 0.001 TYR C 130 PHE 0.015 0.002 PHE B 32 TRP 0.009 0.001 TRP C 117 HIS 0.002 0.001 HIS F 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.20 (20088) covalent geometry : angle 0.66829 / 0.44 (27324) SS BOND : bond 0.02210 / 1.45 ( 24) SS BOND : angle 1.11765 / 0.74 ( 48) hydrogen bonds : bond 0.30390 / 20.42 ( 1128) hydrogen bonds : angle 8.92783 / 6.36 ( 3348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.705 Fit side-chains REVERT: A 112 GLN cc_start: 0.7809 (mp-120) cc_final: 0.7564 (mp10) REVERT: C 4 GLN cc_start: 0.7971 (tt0) cc_final: 0.7351 (tm-30) REVERT: D 112 GLN cc_start: 0.7773 (mp-120) cc_final: 0.7489 (mp-120) REVERT: E 4 GLN cc_start: 0.7976 (tt0) cc_final: 0.7334 (tm-30) REVERT: F 112 GLN cc_start: 0.7727 (mp-120) cc_final: 0.7444 (mp10) REVERT: H 112 GLN cc_start: 0.7712 (mp-120) cc_final: 0.7432 (mp10) REVERT: J 39 MET cc_start: 0.8717 (tpt) cc_final: 0.8516 (tpp) REVERT: J 112 GLN cc_start: 0.7777 (mp-120) cc_final: 0.7490 (mp-120) REVERT: K 112 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7469 (mp10) REVERT: L 4 GLN cc_start: 0.7971 (tt0) cc_final: 0.7339 (tm-30) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1330 time to fit residues: 76.0603 Evaluate side-chains 280 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 193 ASN B 4 GLN B 112 GLN B 193 ASN C 112 GLN C 176 GLN C 193 ASN D 4 GLN D 193 ASN E 176 GLN E 193 ASN F 4 GLN F 176 GLN F 193 ASN G 4 GLN G 112 GLN G 193 ASN H 4 GLN H 176 GLN H 193 ASN I 4 GLN I 112 GLN I 176 GLN I 193 ASN J 4 GLN J 193 ASN K 4 GLN K 193 ASN L 193 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.181142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126172 restraints weight = 20831.176| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.65 r_work: 0.3283 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 20112 Z= 0.277 Angle : 0.648 5.938 27372 Z= 0.336 Chirality : 0.049 0.174 3168 Planarity : 0.006 0.038 3552 Dihedral : 4.553 22.282 2784 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.00 % Allowed : 8.93 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.14), residues: 2604 helix: -1.39 (0.11), residues: 1716 sheet: None (None), residues: 0 loop : -1.73 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 167 TYR 0.019 0.003 TYR J 130 PHE 0.015 0.003 PHE A 32 TRP 0.011 0.002 TRP B 80 HIS 0.004 0.001 HIS E 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.28 (20088) covalent geometry : angle 0.64725 / 0.34 (27324) SS BOND : bond 0.00168 / 0.11 ( 24) SS BOND : angle 0.93170 / 0.65 ( 48) hydrogen bonds : bond 0.05491 / 3.68 ( 1128) hydrogen bonds : angle 4.66516 / 3.29 ( 3348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 295 time to evaluate : 0.745 Fit side-chains REVERT: A 33 SER cc_start: 0.8973 (m) cc_final: 0.8732 (t) REVERT: A 144 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8246 (ttt) REVERT: A 154 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.7385 (mtt-85) REVERT: C 118 MET cc_start: 0.8868 (mtt) cc_final: 0.8632 (mtt) REVERT: D 112 GLN cc_start: 0.7668 (mp-120) cc_final: 0.7413 (mp10) REVERT: J 112 GLN cc_start: 0.7672 (mp-120) cc_final: 0.7418 (mp10) outliers start: 20 outliers final: 15 residues processed: 305 average time/residue: 0.1475 time to fit residues: 68.5145 Evaluate side-chains 299 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 283 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [78, 242, 219, 28, 18, 94, 103, 135, 13, 88, 59] chunk 78 optimal weight: 8.9990 chunk 242 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 0.0020 chunk 135 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 4 GLN E 4 GLN I 176 GLN L 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.187159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132582 restraints weight = 20389.836| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.63 r_work: 0.3358 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20112 Z= 0.095 Angle : 0.458 5.625 27372 Z= 0.233 Chirality : 0.041 0.136 3168 Planarity : 0.004 0.037 3552 Dihedral : 4.054 18.981 2784 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.80 % Allowed : 10.88 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2604 helix: 0.07 (0.12), residues: 1656 sheet: None (None), residues: 0 loop : -1.50 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 167 TYR 0.010 0.001 TYR D 169 PHE 0.010 0.001 PHE H 32 TRP 0.007 0.001 TRP E 23 HIS 0.001 0.000 HIS K 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (20088) covalent geometry : angle 0.45829 / 0.23 (27324) SS BOND : bond 0.00073 / 0.05 ( 24) SS BOND : angle 0.45439 / 0.32 ( 48) hydrogen bonds : bond 0.03570 / 2.41 ( 1128) hydrogen bonds : angle 4.02844 / 2.85 ( 3348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 0.715 Fit side-chains REVERT: C 82 ARG cc_start: 0.7280 (ttp80) cc_final: 0.7061 (ttp80) REVERT: C 118 MET cc_start: 0.8589 (mtt) cc_final: 0.8364 (mtt) REVERT: E 82 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7215 (ttp80) REVERT: E 118 MET cc_start: 0.8582 (mtt) cc_final: 0.8362 (mtt) REVERT: I 82 ARG cc_start: 0.7588 (ttp80) cc_final: 0.7184 (ttp80) REVERT: I 118 MET cc_start: 0.8559 (mtt) cc_final: 0.8301 (mtt) REVERT: L 118 MET cc_start: 0.8581 (mtt) cc_final: 0.8361 (mtt) outliers start: 16 outliers final: 13 residues processed: 308 average time/residue: 0.1482 time to fit residues: 69.8936 Evaluate side-chains 290 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 277 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain L residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [198, 56, 145, 171, 46, 101, 192, 52, 36, 20, 207] chunk 198 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 171 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN F 4 GLN F 176 GLN H 4 GLN H 176 GLN K 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.187126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132851 restraints weight = 20394.893| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.64 r_work: 0.3357 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20112 Z= 0.101 Angle : 0.435 4.515 27372 Z= 0.220 Chirality : 0.041 0.129 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.930 19.233 2784 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.00 % Allowed : 11.83 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2604 helix: 0.73 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.47 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 154 TYR 0.009 0.001 TYR A 169 PHE 0.011 0.002 PHE A 32 TRP 0.006 0.001 TRP A 23 HIS 0.001 0.001 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (20088) covalent geometry : angle 0.43493 / 0.22 (27324) SS BOND : bond 0.00087 / 0.06 ( 24) SS BOND : angle 0.54557 / 0.39 ( 48) hydrogen bonds : bond 0.03169 / 2.13 ( 1128) hydrogen bonds : angle 3.88236 / 2.75 ( 3348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 0.798 Fit side-chains REVERT: C 82 ARG cc_start: 0.7424 (ttp80) cc_final: 0.7165 (ttp80) REVERT: C 103 ASP cc_start: 0.8456 (m-30) cc_final: 0.8223 (m-30) REVERT: C 118 MET cc_start: 0.8575 (mtt) cc_final: 0.8370 (mtt) REVERT: E 103 ASP cc_start: 0.8493 (m-30) cc_final: 0.8255 (m-30) REVERT: J 25 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8107 (mmtm) REVERT: L 103 ASP cc_start: 0.8475 (m-30) cc_final: 0.8242 (m-30) outliers start: 20 outliers final: 16 residues processed: 290 average time/residue: 0.1445 time to fit residues: 64.0337 Evaluate side-chains 295 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [200, 189, 134, 10, 50, 113, 177, 95, 225, 247, 91] chunk 200 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 177 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 chunk 225 optimal weight: 0.0040 chunk 247 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN E 176 GLN F 4 GLN F 176 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135582 restraints weight = 20306.091| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.64 r_work: 0.3380 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20112 Z= 0.085 Angle : 0.406 4.371 27372 Z= 0.205 Chirality : 0.040 0.130 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.802 19.464 2784 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.70 % Allowed : 11.13 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2604 helix: 1.13 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.44 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 154 TYR 0.009 0.001 TYR D 169 PHE 0.010 0.001 PHE H 32 TRP 0.006 0.001 TRP C 23 HIS 0.001 0.000 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.08 (20088) covalent geometry : angle 0.40612 / 0.21 (27324) SS BOND : bond 0.00054 / 0.03 ( 24) SS BOND : angle 0.47683 / 0.34 ( 48) hydrogen bonds : bond 0.02843 / 1.93 ( 1128) hydrogen bonds : angle 3.78828 / 2.68 ( 3348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.695 Fit side-chains REVERT: C 82 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7205 (ttp80) REVERT: C 103 ASP cc_start: 0.8495 (m-30) cc_final: 0.8278 (m-30) REVERT: C 118 MET cc_start: 0.8524 (mtt) cc_final: 0.8307 (mtt) REVERT: E 82 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7153 (ttp80) REVERT: E 103 ASP cc_start: 0.8477 (m-30) cc_final: 0.8248 (m-30) REVERT: I 82 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7166 (ttp80) REVERT: I 103 ASP cc_start: 0.8478 (m-30) cc_final: 0.8257 (m-30) REVERT: J 25 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8137 (mmtm) REVERT: L 103 ASP cc_start: 0.8473 (m-30) cc_final: 0.8250 (m-30) outliers start: 34 outliers final: 18 residues processed: 317 average time/residue: 0.1406 time to fit residues: 68.5738 Evaluate side-chains 312 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 294 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [93, 213, 167, 138, 1, 225, 136, 53, 6, 131, 204] chunk 93 optimal weight: 8.9990 chunk 213 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 0.0010 chunk 1 optimal weight: 3.9990 chunk 225 optimal weight: 0.0870 chunk 136 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN F 4 GLN F 176 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.189466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135508 restraints weight = 20281.735| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.66 r_work: 0.3400 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20112 Z= 0.079 Angle : 0.399 4.372 27372 Z= 0.201 Chirality : 0.040 0.126 3168 Planarity : 0.004 0.040 3552 Dihedral : 3.716 19.618 2784 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 11.48 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2604 helix: 1.38 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.43 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 154 TYR 0.009 0.001 TYR D 169 PHE 0.010 0.001 PHE H 32 TRP 0.006 0.001 TRP B 23 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (20088) covalent geometry : angle 0.39908 / 0.20 (27324) SS BOND : bond 0.00087 / 0.06 ( 24) SS BOND : angle 0.34964 / 0.24 ( 48) hydrogen bonds : bond 0.02632 / 1.78 ( 1128) hydrogen bonds : angle 3.73476 / 2.65 ( 3348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 310 time to evaluate : 0.781 Fit side-chains REVERT: C 82 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7232 (ttp80) REVERT: C 103 ASP cc_start: 0.8506 (m-30) cc_final: 0.8274 (m-30) REVERT: C 118 MET cc_start: 0.8492 (mtt) cc_final: 0.8249 (mtt) REVERT: E 103 ASP cc_start: 0.8505 (m-30) cc_final: 0.8259 (m-30) REVERT: H 53 ASN cc_start: 0.8622 (m-40) cc_final: 0.8377 (m-40) REVERT: I 103 ASP cc_start: 0.8520 (m-30) cc_final: 0.8276 (m-30) REVERT: L 103 ASP cc_start: 0.8517 (m-30) cc_final: 0.8293 (m-30) outliers start: 30 outliers final: 18 residues processed: 316 average time/residue: 0.1531 time to fit residues: 72.8564 Evaluate side-chains 311 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [207, 2, 120, 155, 116, 146, 211, 129, 110, 106, 250] chunk 207 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 155 optimal weight: 0.0030 chunk 116 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 110 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN C 4 GLN F 4 GLN F 176 GLN H 4 GLN I 4 GLN K 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.188552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134249 restraints weight = 20495.205| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.69 r_work: 0.3381 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20112 Z= 0.089 Angle : 0.407 4.371 27372 Z= 0.205 Chirality : 0.041 0.127 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.714 19.448 2784 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.20 % Allowed : 11.88 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2604 helix: 1.50 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.38 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 154 TYR 0.009 0.001 TYR D 169 PHE 0.011 0.001 PHE A 32 TRP 0.005 0.001 TRP H 23 HIS 0.001 0.000 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (20088) covalent geometry : angle 0.40712 / 0.21 (27324) SS BOND : bond 0.00061 / 0.04 ( 24) SS BOND : angle 0.32082 / 0.22 ( 48) hydrogen bonds : bond 0.02780 / 1.88 ( 1128) hydrogen bonds : angle 3.75283 / 2.66 ( 3348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 0.680 Fit side-chains REVERT: A 175 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6947 (tt0) REVERT: C 103 ASP cc_start: 0.8529 (m-30) cc_final: 0.8313 (m-30) REVERT: C 118 MET cc_start: 0.8474 (mtt) cc_final: 0.8236 (mtt) REVERT: E 103 ASP cc_start: 0.8479 (m-30) cc_final: 0.8247 (m-30) REVERT: I 103 ASP cc_start: 0.8505 (m-30) cc_final: 0.8272 (m-30) REVERT: J 25 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8011 (mmtm) REVERT: L 103 ASP cc_start: 0.8508 (m-30) cc_final: 0.8285 (m-30) outliers start: 24 outliers final: 23 residues processed: 311 average time/residue: 0.1583 time to fit residues: 73.7025 Evaluate side-chains 323 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [160, 170, 121, 143, 17, 45, 65, 103, 233, 116, 41] chunk 160 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 143 optimal weight: 0.0470 chunk 17 optimal weight: 9.9990 chunk 45 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN F 4 GLN F 176 GLN H 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.188808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134741 restraints weight = 20490.201| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.67 r_work: 0.3388 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20112 Z= 0.084 Angle : 0.405 4.370 27372 Z= 0.204 Chirality : 0.040 0.126 3168 Planarity : 0.004 0.040 3552 Dihedral : 3.678 19.409 2784 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.40 % Allowed : 12.43 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2604 helix: 1.60 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.34 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.009 0.001 TYR F 169 PHE 0.011 0.001 PHE H 32 TRP 0.005 0.001 TRP H 23 HIS 0.001 0.000 HIS J 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.08 (20088) covalent geometry : angle 0.40519 / 0.20 (27324) SS BOND : bond 0.00070 / 0.04 ( 24) SS BOND : angle 0.33289 / 0.22 ( 48) hydrogen bonds : bond 0.02706 / 1.83 ( 1128) hydrogen bonds : angle 3.73473 / 2.65 ( 3348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 0.660 Fit side-chains REVERT: A 175 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6906 (tt0) REVERT: C 103 ASP cc_start: 0.8506 (m-30) cc_final: 0.8301 (m-30) REVERT: C 118 MET cc_start: 0.8507 (mtt) cc_final: 0.8274 (mtt) REVERT: C 121 ASN cc_start: 0.7903 (t0) cc_final: 0.6971 (m-40) REVERT: E 82 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7314 (ttp80) REVERT: E 103 ASP cc_start: 0.8491 (m-30) cc_final: 0.8263 (m-30) REVERT: I 82 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7302 (ttp80) REVERT: I 103 ASP cc_start: 0.8504 (m-30) cc_final: 0.8257 (m-30) REVERT: J 25 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8124 (mmtm) REVERT: K 53 ASN cc_start: 0.8825 (m-40) cc_final: 0.8462 (m-40) REVERT: L 103 ASP cc_start: 0.8510 (m-30) cc_final: 0.8299 (m-30) outliers start: 28 outliers final: 27 residues processed: 309 average time/residue: 0.1535 time to fit residues: 70.7423 Evaluate side-chains 325 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [157, 203, 198, 173, 19, 34, 208, 182, 177, 20, 71] chunk 157 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 173 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN C 176 GLN E 4 GLN F 4 GLN F 176 GLN H 4 GLN H 176 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129526 restraints weight = 20339.481| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.67 r_work: 0.3317 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20112 Z= 0.146 Angle : 0.462 4.595 27372 Z= 0.233 Chirality : 0.043 0.153 3168 Planarity : 0.005 0.040 3552 Dihedral : 3.873 19.097 2784 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.50 % Allowed : 12.43 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2604 helix: 1.43 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.30 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 154 TYR 0.008 0.001 TYR A 169 PHE 0.013 0.002 PHE H 32 TRP 0.006 0.001 TRP H 23 HIS 0.002 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (20088) covalent geometry : angle 0.46175 / 0.23 (27324) SS BOND : bond 0.00062 / 0.04 ( 24) SS BOND : angle 0.54558 / 0.35 ( 48) hydrogen bonds : bond 0.03375 / 2.27 ( 1128) hydrogen bonds : angle 3.87816 / 2.74 ( 3348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.696 Fit side-chains REVERT: C 82 ARG cc_start: 0.7411 (ttp80) cc_final: 0.7099 (ttp80) REVERT: C 103 ASP cc_start: 0.8437 (m-30) cc_final: 0.8219 (m-30) REVERT: C 118 MET cc_start: 0.8616 (mtt) cc_final: 0.8404 (mtt) REVERT: E 103 ASP cc_start: 0.8509 (m-30) cc_final: 0.8275 (m-30) REVERT: I 103 ASP cc_start: 0.8507 (m-30) cc_final: 0.8265 (m-30) REVERT: L 103 ASP cc_start: 0.8454 (m-30) cc_final: 0.8229 (m-30) outliers start: 30 outliers final: 28 residues processed: 293 average time/residue: 0.1544 time to fit residues: 67.8517 Evaluate side-chains 307 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [76, 29, 10, 226, 85, 166, 154, 40, 59, 147, 73] chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 73 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN C 176 GLN F 4 GLN F 176 GLN H 4 GLN H 176 GLN K 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.186548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131583 restraints weight = 20431.370| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.67 r_work: 0.3351 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20112 Z= 0.099 Angle : 0.428 4.411 27372 Z= 0.216 Chirality : 0.041 0.130 3168 Planarity : 0.004 0.040 3552 Dihedral : 3.794 19.504 2784 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.45 % Allowed : 12.57 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2604 helix: 1.56 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.31 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.009 0.001 TYR A 169 PHE 0.009 0.001 PHE H 32 TRP 0.005 0.001 TRP D 23 HIS 0.001 0.000 HIS B 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (20088) covalent geometry : angle 0.42809 / 0.22 (27324) SS BOND : bond 0.00084 / 0.05 ( 24) SS BOND : angle 0.48346 / 0.31 ( 48) hydrogen bonds : bond 0.02984 / 2.01 ( 1128) hydrogen bonds : angle 3.81503 / 2.70 ( 3348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.500 Fit side-chains REVERT: C 103 ASP cc_start: 0.8480 (m-30) cc_final: 0.8262 (m-30) REVERT: C 118 MET cc_start: 0.8544 (mtt) cc_final: 0.8343 (mtt) REVERT: E 103 ASP cc_start: 0.8489 (m-30) cc_final: 0.8265 (m-30) REVERT: I 103 ASP cc_start: 0.8515 (m-30) cc_final: 0.8267 (m-30) REVERT: L 103 ASP cc_start: 0.8481 (m-30) cc_final: 0.8264 (m-30) outliers start: 29 outliers final: 25 residues processed: 296 average time/residue: 0.1565 time to fit residues: 68.5511 Evaluate side-chains 311 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: [231, 112, 240, 116, 95, 70, 8, 48, 27, 63, 165] chunk 231 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN C 176 GLN F 4 GLN F 176 GLN H 4 GLN H 176 GLN K 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129691 restraints weight = 20537.058| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.68 r_work: 0.3324 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20112 Z= 0.128 Angle : 0.450 4.493 27372 Z= 0.226 Chirality : 0.043 0.132 3168 Planarity : 0.004 0.040 3552 Dihedral : 3.872 19.406 2784 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.50 % Allowed : 12.67 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2604 helix: 1.50 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.35 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 154 TYR 0.008 0.001 TYR A 169 PHE 0.011 0.002 PHE H 32 TRP 0.005 0.001 TRP D 23 HIS 0.003 0.001 HIS I 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (20088) covalent geometry : angle 0.45017 / 0.23 (27324) SS BOND : bond 0.00087 / 0.06 ( 24) SS BOND : angle 0.50172 / 0.32 ( 48) hydrogen bonds : bond 0.03258 / 2.19 ( 1128) hydrogen bonds : angle 3.88533 / 2.75 ( 3348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.04 seconds wall clock time: 72 minutes 6.09 seconds (4326.09 seconds total)