Starting phenix.real_space_refine on Tue Jun 17 04:15:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ja0_61286/06_2025/9ja0_61286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ja0_61286/06_2025/9ja0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ja0_61286/06_2025/9ja0_61286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ja0_61286/06_2025/9ja0_61286.map" model { file = "/net/cci-nas-00/data/ceres_data/9ja0_61286/06_2025/9ja0_61286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ja0_61286/06_2025/9ja0_61286.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 6.59, per 1000 atoms: 0.33 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 E 14 " - pdb=" SG CYS F 45 " distance=2.00 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS C 45 " distance=2.01 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS L 45 " distance=2.01 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS D 45 " distance=2.00 Simple disulfide: pdb=" SG CYS I 14 " - pdb=" SG CYS H 45 " distance=2.00 Simple disulfide: pdb=" SG CYS H 14 " - pdb=" SG CYS G 45 " distance=2.01 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS J 45 " distance=2.01 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS I 45 " distance=2.01 Simple disulfide: pdb=" SG CYS L 14 " - pdb=" SG CYS K 45 " distance=2.01 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.03 Simple disulfide: pdb=" SG CYS I 198 " - pdb=" SG CYS I 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS K 198 " - pdb=" SG CYS K 218 " distance=2.03 Simple disulfide: pdb=" SG CYS J 198 " - pdb=" SG CYS J 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: 5.01 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.95 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: 5.86 Time building geometry restraints manager: 5.95 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: 217 41.34 - 55.12: 95 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 39.820 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 8.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (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 TRP 0.009 0.001 TRP C 117 HIS 0.002 0.001 HIS F 12 PHE 0.015 0.002 PHE B 32 TYR 0.006 0.001 TYR C 130 ARG 0.003 0.001 ARG F 154 Details of bonding type rmsd hydrogen bonds : bond 0.30390 ( 1128) hydrogen bonds : angle 8.92783 ( 3348) SS BOND : bond 0.02210 ( 24) SS BOND : angle 1.11765 ( 48) covalent geometry : bond 0.00340 (20088) covalent geometry : angle 0.66829 (27324) *********************** 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 : 2.276 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: 0.3067 time to fit residues: 171.8417 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 : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 0.0570 chunk 228 optimal weight: 8.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 193 ASN B 4 GLN B 112 GLN B 193 ASN C 112 GLN C 193 ASN D 4 GLN D 193 ASN E 193 ASN F 4 GLN F 193 ASN G 4 GLN G 112 GLN G 193 ASN H 4 GLN H 193 ASN I 4 GLN I 112 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130101 restraints weight = 20627.524| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.65 r_work: 0.3342 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20112 Z= 0.182 Angle : 0.564 5.890 27372 Z= 0.294 Chirality : 0.045 0.131 3168 Planarity : 0.005 0.039 3552 Dihedral : 4.239 19.696 2784 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.75 % Allowed : 7.29 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 2604 helix: -0.99 (0.11), residues: 1644 sheet: None (None), residues: 0 loop : -1.52 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 117 HIS 0.003 0.001 HIS E 84 PHE 0.014 0.002 PHE A 32 TYR 0.015 0.002 TYR K 130 ARG 0.003 0.001 ARG H 167 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 1128) hydrogen bonds : angle 4.42042 ( 3348) SS BOND : bond 0.00055 ( 24) SS BOND : angle 0.80436 ( 48) covalent geometry : bond 0.00442 (20088) covalent geometry : angle 0.56344 (27324) *********************** 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 301 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 286 time to evaluate : 2.156 Fit side-chains REVERT: A 33 SER cc_start: 0.8970 (m) cc_final: 0.8674 (t) REVERT: B 82 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7152 (ttp80) REVERT: C 82 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7183 (ttp80) REVERT: D 82 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7167 (ttp80) REVERT: E 82 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7221 (ttp80) REVERT: F 82 ARG cc_start: 0.7372 (ttp80) cc_final: 0.7170 (ttp80) REVERT: G 82 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7135 (ttp80) REVERT: J 82 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7096 (ttp80) REVERT: K 82 ARG cc_start: 0.7343 (ttp80) cc_final: 0.7142 (ttp80) outliers start: 15 outliers final: 15 residues processed: 292 average time/residue: 0.3231 time to fit residues: 143.2247 Evaluate side-chains 300 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 285 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 11 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G 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 J residue 11 VAL 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: chunk 68 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 133 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 4 GLN E 4 GLN F 4 GLN H 4 GLN K 4 GLN L 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.187567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132469 restraints weight = 20468.991| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.67 r_work: 0.3362 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2206 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= 0.105 Angle : 0.453 5.141 27372 Z= 0.232 Chirality : 0.041 0.135 3168 Planarity : 0.004 0.038 3552 Dihedral : 3.958 18.910 2784 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.45 % Allowed : 9.88 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2604 helix: 0.19 (0.12), residues: 1656 sheet: None (None), residues: 0 loop : -1.43 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 23 HIS 0.001 0.000 HIS J 12 PHE 0.010 0.002 PHE H 32 TYR 0.009 0.001 TYR D 169 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1128) hydrogen bonds : angle 3.99076 ( 3348) SS BOND : bond 0.00086 ( 24) SS BOND : angle 0.45726 ( 48) covalent geometry : bond 0.00237 (20088) covalent geometry : angle 0.45333 (27324) *********************** 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 294 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 285 time to evaluate : 2.177 Fit side-chains REVERT: C 82 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7119 (ttp80) REVERT: I 82 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7297 (ttp80) REVERT: L 82 ARG cc_start: 0.7300 (ttp80) cc_final: 0.7095 (ttp80) outliers start: 9 outliers final: 6 residues processed: 292 average time/residue: 0.3445 time to fit residues: 152.9495 Evaluate side-chains 275 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 269 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain K residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 222 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 45 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 210 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 overall best weight: 0.4872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 4 GLN E 4 GLN F 4 GLN H 4 GLN K 4 GLN L 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136103 restraints weight = 20447.102| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.62 r_work: 0.3388 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2400 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= 0.090 Angle : 0.416 4.450 27372 Z= 0.211 Chirality : 0.041 0.126 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.851 19.429 2784 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.30 % Allowed : 10.33 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2604 helix: 0.84 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.38 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 23 HIS 0.001 0.000 HIS G 12 PHE 0.011 0.001 PHE A 32 TYR 0.009 0.001 TYR A 169 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 1128) hydrogen bonds : angle 3.77492 ( 3348) SS BOND : bond 0.00070 ( 24) SS BOND : angle 0.58175 ( 48) covalent geometry : bond 0.00207 (20088) covalent geometry : angle 0.41517 (27324) *********************** 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 322 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 2.421 Fit side-chains REVERT: C 82 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7146 (ttp80) REVERT: C 103 ASP cc_start: 0.8584 (m-30) cc_final: 0.8286 (m-30) REVERT: E 103 ASP cc_start: 0.8602 (m-30) cc_final: 0.8303 (m-30) REVERT: I 82 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7153 (ttp80) REVERT: I 103 ASP cc_start: 0.8599 (m-30) cc_final: 0.8282 (m-30) REVERT: L 82 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7119 (ttp80) REVERT: L 103 ASP cc_start: 0.8579 (m-30) cc_final: 0.8280 (m-30) outliers start: 26 outliers final: 19 residues processed: 305 average time/residue: 0.3298 time to fit residues: 153.4158 Evaluate side-chains 306 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET 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 102 SER Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 11 VAL 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 11 VAL Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 11 VAL 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: chunk 128 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 GLN E 4 GLN F 4 GLN H 4 GLN I 4 GLN K 4 GLN L 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131140 restraints weight = 20596.375| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.67 r_work: 0.3347 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20112 Z= 0.119 Angle : 0.433 4.456 27372 Z= 0.219 Chirality : 0.042 0.133 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.882 19.321 2784 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.05 % Allowed : 10.78 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2604 helix: 1.05 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.46 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 23 HIS 0.002 0.001 HIS D 84 PHE 0.012 0.002 PHE A 32 TYR 0.009 0.001 TYR A 169 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 1128) hydrogen bonds : angle 3.84549 ( 3348) SS BOND : bond 0.00107 ( 24) SS BOND : angle 0.46199 ( 48) covalent geometry : bond 0.00291 (20088) covalent geometry : angle 0.43328 (27324) *********************** 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 306 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 285 time to evaluate : 2.123 Fit side-chains REVERT: C 82 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7211 (ttp80) REVERT: C 103 ASP cc_start: 0.8567 (m-30) cc_final: 0.8263 (m-30) REVERT: E 82 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7125 (ttp80) REVERT: E 103 ASP cc_start: 0.8584 (m-30) cc_final: 0.8278 (m-30) REVERT: I 103 ASP cc_start: 0.8593 (m-30) cc_final: 0.8290 (m-30) REVERT: L 82 ARG cc_start: 0.7434 (ttp80) cc_final: 0.7159 (ttp80) REVERT: L 103 ASP cc_start: 0.8570 (m-30) cc_final: 0.8263 (m-30) outliers start: 21 outliers final: 18 residues processed: 287 average time/residue: 0.3367 time to fit residues: 147.1217 Evaluate side-chains 296 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 278 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 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 11 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL 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 11 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 57 optimal weight: 0.0570 chunk 213 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 86 optimal weight: 0.0570 chunk 239 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN F 4 GLN H 4 GLN K 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 = 0.188827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134642 restraints weight = 20380.044| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.67 r_work: 0.3390 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2604 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= 0.081 Angle : 0.402 4.291 27372 Z= 0.203 Chirality : 0.040 0.127 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.752 19.677 2784 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.35 % Allowed : 10.63 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2604 helix: 1.35 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.43 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 23 HIS 0.001 0.000 HIS G 12 PHE 0.009 0.001 PHE H 32 TYR 0.009 0.001 TYR A 169 ARG 0.007 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 1128) hydrogen bonds : angle 3.73730 ( 3348) SS BOND : bond 0.00066 ( 24) SS BOND : angle 0.39788 ( 48) covalent geometry : bond 0.00190 (20088) covalent geometry : angle 0.40229 (27324) *********************** 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 324 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 2.290 Fit side-chains REVERT: C 82 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7172 (ttp80) REVERT: C 103 ASP cc_start: 0.8577 (m-30) cc_final: 0.8307 (m-30) REVERT: E 103 ASP cc_start: 0.8592 (m-30) cc_final: 0.8317 (m-30) REVERT: G 82 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7243 (ttp80) REVERT: I 103 ASP cc_start: 0.8602 (m-30) cc_final: 0.8301 (m-30) REVERT: J 25 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8112 (mmtm) REVERT: L 82 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7178 (ttp80) REVERT: L 103 ASP cc_start: 0.8600 (m-30) cc_final: 0.8319 (m-30) outliers start: 27 outliers final: 19 residues processed: 300 average time/residue: 0.3267 time to fit residues: 147.1005 Evaluate side-chains 300 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 281 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 144 MET 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 11 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 66 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 11 VAL Chi-restraints excluded: chain K residue 66 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 192 optimal weight: 0.0060 chunk 197 optimal weight: 0.0040 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 182 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 4 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135060 restraints weight = 20166.131| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.59 r_work: 0.3403 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2692 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= 0.081 Angle : 0.403 4.372 27372 Z= 0.203 Chirality : 0.040 0.125 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.697 19.643 2784 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.95 % Allowed : 11.78 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2604 helix: 1.54 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.40 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 23 HIS 0.001 0.000 HIS A 12 PHE 0.010 0.001 PHE H 32 TYR 0.009 0.001 TYR A 169 ARG 0.007 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.02697 ( 1128) hydrogen bonds : angle 3.70025 ( 3348) SS BOND : bond 0.00068 ( 24) SS BOND : angle 0.34375 ( 48) covalent geometry : bond 0.00186 (20088) covalent geometry : angle 0.40310 (27324) *********************** 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 316 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 2.120 Fit side-chains REVERT: C 103 ASP cc_start: 0.8584 (m-30) cc_final: 0.8290 (m-30) REVERT: E 82 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7242 (ttp80) REVERT: E 103 ASP cc_start: 0.8595 (m-30) cc_final: 0.8324 (m-30) REVERT: I 82 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7324 (ttp80) REVERT: I 103 ASP cc_start: 0.8575 (m-30) cc_final: 0.8283 (m-30) REVERT: J 25 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8131 (mmtm) REVERT: L 82 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7218 (ttp80) REVERT: L 103 ASP cc_start: 0.8581 (m-30) cc_final: 0.8305 (m-30) outliers start: 19 outliers final: 17 residues processed: 298 average time/residue: 0.3268 time to fit residues: 146.2313 Evaluate side-chains 306 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 66 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 11 VAL Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain K residue 144 MET 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: chunk 250 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 225 optimal weight: 0.5980 chunk 216 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 4 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129778 restraints weight = 20593.914| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.67 r_work: 0.3311 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20112 Z= 0.143 Angle : 0.454 4.593 27372 Z= 0.229 Chirality : 0.043 0.133 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.889 19.293 2784 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.30 % Allowed : 11.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2604 helix: 1.39 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.38 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 23 HIS 0.002 0.001 HIS C 84 PHE 0.013 0.002 PHE H 32 TYR 0.008 0.001 TYR A 169 ARG 0.006 0.001 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 1128) hydrogen bonds : angle 3.88207 ( 3348) SS BOND : bond 0.00092 ( 24) SS BOND : angle 0.34571 ( 48) covalent geometry : bond 0.00354 (20088) covalent geometry : angle 0.45436 (27324) *********************** 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 309 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 2.319 Fit side-chains REVERT: C 82 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7290 (ttp80) REVERT: C 103 ASP cc_start: 0.8572 (m-30) cc_final: 0.8315 (m-30) REVERT: E 103 ASP cc_start: 0.8576 (m-30) cc_final: 0.8320 (m-30) REVERT: I 103 ASP cc_start: 0.8593 (m-30) cc_final: 0.8321 (m-30) REVERT: L 82 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7235 (ttp80) REVERT: L 103 ASP cc_start: 0.8567 (m-30) cc_final: 0.8310 (m-30) outliers start: 26 outliers final: 22 residues processed: 289 average time/residue: 0.3647 time to fit residues: 156.3880 Evaluate side-chains 301 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 136 LEU 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 11 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 66 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 11 VAL Chi-restraints excluded: chain K residue 66 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 197 optimal weight: 0.0870 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN F 4 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131259 restraints weight = 20446.665| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.65 r_work: 0.3346 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20112 Z= 0.108 Angle : 0.429 4.396 27372 Z= 0.216 Chirality : 0.042 0.130 3168 Planarity : 0.004 0.039 3552 Dihedral : 3.798 19.566 2784 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.20 % Allowed : 11.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2604 helix: 1.49 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.34 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 23 HIS 0.002 0.000 HIS K 84 PHE 0.009 0.001 PHE H 32 TYR 0.009 0.001 TYR A 169 ARG 0.007 0.000 ARG F 154 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 1128) hydrogen bonds : angle 3.83174 ( 3348) SS BOND : bond 0.00075 ( 24) SS BOND : angle 0.36203 ( 48) covalent geometry : bond 0.00263 (20088) covalent geometry : angle 0.42914 (27324) *********************** 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 307 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 2.072 Fit side-chains REVERT: C 82 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7196 (ttp80) REVERT: C 103 ASP cc_start: 0.8539 (m-30) cc_final: 0.8307 (m-30) REVERT: C 154 ARG cc_start: 0.7533 (mtt-85) cc_final: 0.7238 (mtt-85) REVERT: E 82 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7183 (ttp80) REVERT: E 103 ASP cc_start: 0.8556 (m-30) cc_final: 0.8300 (m-30) REVERT: E 154 ARG cc_start: 0.7514 (mtt-85) cc_final: 0.7224 (mtt-85) REVERT: I 103 ASP cc_start: 0.8576 (m-30) cc_final: 0.8312 (m-30) REVERT: I 154 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7219 (mtt-85) REVERT: L 82 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7252 (ttp80) REVERT: L 103 ASP cc_start: 0.8553 (m-30) cc_final: 0.8303 (m-30) REVERT: L 154 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.7233 (mtt-85) outliers start: 24 outliers final: 21 residues processed: 284 average time/residue: 0.3604 time to fit residues: 149.7747 Evaluate side-chains 302 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 136 LEU 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 11 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 66 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 11 VAL Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain K residue 144 MET 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: chunk 127 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN F 4 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.185341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130050 restraints weight = 20361.235| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.67 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20112 Z= 0.121 Angle : 0.440 4.504 27372 Z= 0.221 Chirality : 0.042 0.132 3168 Planarity : 0.004 0.038 3552 Dihedral : 3.840 19.518 2784 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.05 % Allowed : 11.98 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2604 helix: 1.49 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.37 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 23 HIS 0.002 0.001 HIS I 84 PHE 0.011 0.002 PHE H 32 TYR 0.008 0.001 TYR A 169 ARG 0.007 0.001 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 1128) hydrogen bonds : angle 3.85248 ( 3348) SS BOND : bond 0.00090 ( 24) SS BOND : angle 0.36811 ( 48) covalent geometry : bond 0.00296 (20088) covalent geometry : angle 0.43996 (27324) ********************** 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 299 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 2.449 Fit side-chains REVERT: A 175 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6793 (tt0) REVERT: C 82 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7252 (ttp80) REVERT: C 103 ASP cc_start: 0.8540 (m-30) cc_final: 0.8276 (m-30) REVERT: E 103 ASP cc_start: 0.8535 (m-30) cc_final: 0.8292 (m-30) REVERT: L 82 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7253 (ttp80) REVERT: L 103 ASP cc_start: 0.8549 (m-30) cc_final: 0.8293 (m-30) outliers start: 21 outliers final: 21 residues processed: 281 average time/residue: 0.3578 time to fit residues: 147.5760 Evaluate side-chains 299 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 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 11 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 66 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 11 VAL Chi-restraints excluded: chain K residue 66 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN E 4 GLN F 4 GLN H 4 GLN L 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131202 restraints weight = 20516.239| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.67 r_work: 0.3344 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20112 Z= 0.105 Angle : 0.432 4.404 27372 Z= 0.217 Chirality : 0.042 0.131 3168 Planarity : 0.005 0.039 3552 Dihedral : 3.808 19.618 2784 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.30 % Allowed : 12.23 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2604 helix: 1.58 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.37 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 23 HIS 0.002 0.000 HIS E 84 PHE 0.009 0.001 PHE G 32 TYR 0.009 0.001 TYR A 169 ARG 0.009 0.001 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 1128) hydrogen bonds : angle 3.82896 ( 3348) SS BOND : bond 0.00079 ( 24) SS BOND : angle 0.37094 ( 48) covalent geometry : bond 0.00253 (20088) covalent geometry : angle 0.43179 (27324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9112.93 seconds wall clock time: 157 minutes 1.08 seconds (9421.08 seconds total)