Starting phenix.real_space_refine on Sun May 18 09:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2v_47469/05_2025/9e2v_47469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2v_47469/05_2025/9e2v_47469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2v_47469/05_2025/9e2v_47469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2v_47469/05_2025/9e2v_47469.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2v_47469/05_2025/9e2v_47469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2v_47469/05_2025/9e2v_47469.cif" } resolution = 2.0 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= 0.024 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 90 5.16 5 C 10490 2.51 5 N 2950 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16910 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1691 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 7.37, per 1000 atoms: 0.44 Number of scatterers: 16910 At special positions: 0 Unit cell: (119.316, 116.388, 104.676, 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 90 16.00 O 3380 8.00 N 2950 7.00 C 10490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 41.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY A 112 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A 114 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 Processing helix chain 'A' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'B' and resid 23 through 31 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS B 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY B 112 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU B 114 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 159 Processing helix chain 'B' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY C 112 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TRP C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU C 114 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 159 Processing helix chain 'C' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'D' and resid 23 through 31 Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.507A pdb=" N LYS D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY D 112 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TRP D 113 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU D 114 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 Processing helix chain 'D' and resid 224 through 242 removed outlier: 3.571A pdb=" N ALA D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'E' and resid 23 through 31 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY E 112 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP E 113 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU E 114 " --> pdb=" O GLN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 134 removed outlier: 3.736A pdb=" N TYR E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 159 Processing helix chain 'E' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'F' and resid 23 through 31 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS F 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY F 112 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU F 114 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR F 134 " --> pdb=" O GLY F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 159 Processing helix chain 'F' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'G' and resid 23 through 31 Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.507A pdb=" N LYS G 90 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 116 removed outlier: 4.127A pdb=" N GLY G 112 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP G 113 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU G 114 " --> pdb=" O GLN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR G 134 " --> pdb=" O GLY G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 159 Processing helix chain 'G' and resid 224 through 242 removed outlier: 3.573A pdb=" N ALA G 228 " --> pdb=" O LYS G 224 " (cutoff:3.500A) Proline residue: G 230 - end of helix Processing helix chain 'H' and resid 23 through 31 Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 116 removed outlier: 4.127A pdb=" N GLY H 112 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP H 113 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU H 114 " --> pdb=" O GLN H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 159 Processing helix chain 'H' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA H 228 " --> pdb=" O LYS H 224 " (cutoff:3.500A) Proline residue: H 230 - end of helix Processing helix chain 'I' and resid 23 through 31 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS I 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY I 112 " --> pdb=" O GLU I 109 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP I 113 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU I 114 " --> pdb=" O GLN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 134 removed outlier: 3.736A pdb=" N TYR I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 159 Processing helix chain 'I' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA I 228 " --> pdb=" O LYS I 224 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'J' and resid 23 through 31 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.508A pdb=" N LYS J 90 " --> pdb=" O SER J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 116 removed outlier: 4.128A pdb=" N GLY J 112 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP J 113 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU J 114 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 134 removed outlier: 3.737A pdb=" N TYR J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 159 Processing helix chain 'J' and resid 224 through 242 removed outlier: 3.572A pdb=" N ALA J 228 " --> pdb=" O LYS J 224 " (cutoff:3.500A) Proline residue: J 230 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 35 through 40 current: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN A 206 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA A 179 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR A 204 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL A 181 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N THR A 202 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR A 183 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR A 200 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N ASN A 185 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ILE A 198 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA A 187 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA A 196 " --> pdb=" O ALA A 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 195 through 221 current: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN B 206 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA B 179 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N THR B 204 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL B 181 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR B 202 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR B 183 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR B 200 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN B 185 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ILE B 198 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA B 187 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA B 196 " --> pdb=" O ALA B 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 195 through 221 current: chain 'C' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN C 206 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA C 179 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR C 204 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL C 181 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N THR C 202 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N THR C 183 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N THR C 200 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN C 185 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N ILE C 198 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA C 187 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ALA C 196 " --> pdb=" O ALA C 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 195 through 221 current: chain 'D' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 84 current: chain 'D' and resid 162 through 190 removed outlier: 5.310A pdb=" N ASN D 206 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA D 179 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR D 204 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 11.090A pdb=" N VAL D 181 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR D 202 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR D 183 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR D 200 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN D 185 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ILE D 198 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ALA D 187 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ALA D 196 " --> pdb=" O ALA D 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 195 through 221 current: chain 'E' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 83 through 84 current: chain 'E' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN E 206 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA E 179 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N THR E 204 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL E 181 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR E 202 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR E 183 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR E 200 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN E 185 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE E 198 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA E 187 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA E 196 " --> pdb=" O ALA E 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 195 through 221 current: chain 'F' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 83 through 84 current: chain 'F' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN F 206 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA F 179 " --> pdb=" O THR F 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR F 204 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL F 181 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR F 202 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR F 183 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR F 200 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN F 185 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ILE F 198 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA F 187 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA F 196 " --> pdb=" O ALA F 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 195 through 221 current: chain 'G' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 83 through 84 current: chain 'G' and resid 162 through 190 removed outlier: 5.310A pdb=" N ASN G 206 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA G 179 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N THR G 204 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL G 181 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N THR G 202 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR G 183 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR G 200 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N ASN G 185 " --> pdb=" O ILE G 198 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ILE G 198 " --> pdb=" O ASN G 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA G 187 " --> pdb=" O ALA G 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA G 196 " --> pdb=" O ALA G 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 195 through 221 current: chain 'H' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 83 through 84 current: chain 'H' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN H 206 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ALA H 179 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR H 204 " --> pdb=" O ALA H 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL H 181 " --> pdb=" O THR H 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR H 202 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR H 183 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR H 200 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN H 185 " --> pdb=" O ILE H 198 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N ILE H 198 " --> pdb=" O ASN H 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA H 187 " --> pdb=" O ALA H 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA H 196 " --> pdb=" O ALA H 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 195 through 221 current: chain 'I' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 83 through 84 current: chain 'I' and resid 162 through 190 removed outlier: 5.310A pdb=" N ASN I 206 " --> pdb=" O THR I 177 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA I 179 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR I 204 " --> pdb=" O ALA I 179 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL I 181 " --> pdb=" O THR I 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR I 202 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR I 183 " --> pdb=" O THR I 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR I 200 " --> pdb=" O THR I 183 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N ASN I 185 " --> pdb=" O ILE I 198 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ILE I 198 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ALA I 187 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ALA I 196 " --> pdb=" O ALA I 187 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 195 through 221 current: chain 'J' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 83 through 84 current: chain 'J' and resid 162 through 190 removed outlier: 5.309A pdb=" N ASN J 206 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA J 179 " --> pdb=" O THR J 204 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N THR J 204 " --> pdb=" O ALA J 179 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N VAL J 181 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N THR J 202 " --> pdb=" O VAL J 181 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N THR J 183 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N THR J 200 " --> pdb=" O THR J 183 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N ASN J 185 " --> pdb=" O ILE J 198 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N ILE J 198 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ALA J 187 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA J 196 " --> pdb=" O ALA J 187 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 4.68 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: 5720 1.34 - 1.46: 3437 1.46 - 1.58: 7763 1.58 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 17090 Sorted by residual: bond pdb=" CA GLY J 192 " pdb=" C GLY J 192 " ideal model delta sigma weight residual 1.514 1.496 0.019 1.41e-02 5.03e+03 1.77e+00 bond pdb=" CA GLY I 192 " pdb=" C GLY I 192 " ideal model delta sigma weight residual 1.514 1.496 0.018 1.41e-02 5.03e+03 1.68e+00 bond pdb=" CA GLY D 192 " pdb=" C GLY D 192 " ideal model delta sigma weight residual 1.514 1.496 0.018 1.41e-02 5.03e+03 1.68e+00 bond pdb=" CA GLY A 192 " pdb=" C GLY A 192 " ideal model delta sigma weight residual 1.514 1.496 0.018 1.41e-02 5.03e+03 1.65e+00 bond pdb=" CA GLY F 192 " pdb=" C GLY F 192 " ideal model delta sigma weight residual 1.514 1.496 0.018 1.41e-02 5.03e+03 1.63e+00 ... (remaining 17085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 22530 0.99 - 1.99: 450 1.99 - 2.98: 70 2.98 - 3.98: 20 3.98 - 4.97: 20 Bond angle restraints: 23090 Sorted by residual: angle pdb=" N GLY I 195 " pdb=" CA GLY I 195 " pdb=" C GLY I 195 " ideal model delta sigma weight residual 111.04 115.14 -4.10 2.37e+00 1.78e-01 3.00e+00 angle pdb=" N GLY B 195 " pdb=" CA GLY B 195 " pdb=" C GLY B 195 " ideal model delta sigma weight residual 111.04 115.12 -4.08 2.37e+00 1.78e-01 2.97e+00 angle pdb=" N GLY J 195 " pdb=" CA GLY J 195 " pdb=" C GLY J 195 " ideal model delta sigma weight residual 111.04 115.12 -4.08 2.37e+00 1.78e-01 2.96e+00 angle pdb=" N GLY G 195 " pdb=" CA GLY G 195 " pdb=" C GLY G 195 " ideal model delta sigma weight residual 111.04 115.12 -4.08 2.37e+00 1.78e-01 2.96e+00 angle pdb=" N GLY H 195 " pdb=" CA GLY H 195 " pdb=" C GLY H 195 " ideal model delta sigma weight residual 111.04 115.10 -4.06 2.37e+00 1.78e-01 2.93e+00 ... (remaining 23085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 8760 15.63 - 31.26: 1076 31.26 - 46.88: 346 46.88 - 62.51: 168 62.51 - 78.14: 60 Dihedral angle restraints: 10410 sinusoidal: 3950 harmonic: 6460 Sorted by residual: dihedral pdb=" CG LYS H 80 " pdb=" CD LYS H 80 " pdb=" CE LYS H 80 " pdb=" NZ LYS H 80 " ideal model delta sinusoidal sigma weight residual 180.00 125.66 54.34 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CG LYS I 80 " pdb=" CD LYS I 80 " pdb=" CE LYS I 80 " pdb=" NZ LYS I 80 " ideal model delta sinusoidal sigma weight residual 180.00 125.67 54.33 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CG LYS A 80 " pdb=" CD LYS A 80 " pdb=" CE LYS A 80 " pdb=" NZ LYS A 80 " ideal model delta sinusoidal sigma weight residual 180.00 125.69 54.31 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 10407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1473 0.023 - 0.047: 691 0.047 - 0.070: 325 0.070 - 0.093: 61 0.093 - 0.116: 170 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CA VAL C 99 " pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CB VAL C 99 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE B 168 " pdb=" N ILE B 168 " pdb=" C ILE B 168 " pdb=" CB ILE B 168 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 2717 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 137 " -0.002 2.00e-02 2.50e+03 4.83e-03 2.33e-01 pdb=" C ASN E 137 " 0.008 2.00e-02 2.50e+03 pdb=" O ASN E 137 " -0.003 2.00e-02 2.50e+03 pdb=" N SER E 138 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 137 " -0.002 2.00e-02 2.50e+03 4.76e-03 2.27e-01 pdb=" C ASN G 137 " 0.008 2.00e-02 2.50e+03 pdb=" O ASN G 137 " -0.003 2.00e-02 2.50e+03 pdb=" N SER G 138 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 137 " -0.002 2.00e-02 2.50e+03 4.68e-03 2.19e-01 pdb=" C ASN F 137 " 0.008 2.00e-02 2.50e+03 pdb=" O ASN F 137 " -0.003 2.00e-02 2.50e+03 pdb=" N SER F 138 " -0.003 2.00e-02 2.50e+03 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6571 2.88 - 3.39: 15026 3.39 - 3.89: 29818 3.89 - 4.40: 33112 4.40 - 4.90: 55918 Nonbonded interactions: 140445 Sorted by model distance: nonbonded pdb=" O GLY D 112 " pdb=" ND2 ASN D 115 " model vdw 2.381 3.120 nonbonded pdb=" O GLY G 112 " pdb=" ND2 ASN G 115 " model vdw 2.381 3.120 nonbonded pdb=" O GLY J 112 " pdb=" ND2 ASN J 115 " model vdw 2.381 3.120 nonbonded pdb=" O GLY I 112 " pdb=" ND2 ASN I 115 " model vdw 2.381 3.120 nonbonded pdb=" O GLY H 112 " pdb=" ND2 ASN H 115 " model vdw 2.382 3.120 ... (remaining 140440 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: 0.15 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 'J' } 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: 8.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 33.860 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17090 Z= 0.118 Angle : 0.402 4.972 23090 Z= 0.226 Chirality : 0.039 0.116 2720 Planarity : 0.002 0.011 2970 Dihedral : 17.947 78.141 6270 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.85 % Allowed : 24.01 % Favored : 75.14 % 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: 1.64 (0.18), residues: 2240 helix: 1.27 (0.18), residues: 810 sheet: 1.08 (0.18), residues: 830 loop : 1.13 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 45 HIS 0.001 0.000 HIS A 208 PHE 0.006 0.001 PHE D 225 TYR 0.006 0.001 TYR B 93 ARG 0.001 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.19885 ( 731) hydrogen bonds : angle 6.27207 ( 2073) covalent geometry : bond 0.00239 (17090) covalent geometry : angle 0.40199 (23090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.890 Fit side-chains REVERT: A 109 GLU cc_start: 0.8472 (tp30) cc_final: 0.8233 (tp30) REVERT: A 224 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8756 (mmtp) REVERT: B 109 GLU cc_start: 0.8469 (tp30) cc_final: 0.8239 (tp30) REVERT: B 143 LEU cc_start: 0.8071 (mm) cc_final: 0.7583 (tm) REVERT: B 224 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8580 (mttp) REVERT: C 109 GLU cc_start: 0.8392 (tp30) cc_final: 0.8086 (tp30) REVERT: C 143 LEU cc_start: 0.8059 (mm) cc_final: 0.7585 (tm) REVERT: C 224 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8584 (mmtp) REVERT: D 109 GLU cc_start: 0.8550 (tp30) cc_final: 0.8187 (tp30) REVERT: D 224 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8606 (mmtp) REVERT: E 109 GLU cc_start: 0.8472 (tp30) cc_final: 0.8231 (tp30) REVERT: E 143 LEU cc_start: 0.8091 (mm) cc_final: 0.7580 (tm) REVERT: E 224 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8612 (mtpp) REVERT: F 109 GLU cc_start: 0.8482 (tp30) cc_final: 0.8241 (tp30) REVERT: F 224 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8563 (mmtp) REVERT: G 109 GLU cc_start: 0.8494 (tp30) cc_final: 0.8266 (tp30) REVERT: G 143 LEU cc_start: 0.8045 (mm) cc_final: 0.7550 (tm) REVERT: G 224 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8578 (mttp) REVERT: H 109 GLU cc_start: 0.8419 (tp30) cc_final: 0.8127 (tp30) REVERT: H 143 LEU cc_start: 0.8098 (mm) cc_final: 0.7607 (tm) REVERT: H 224 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8624 (mmtp) REVERT: I 109 GLU cc_start: 0.8527 (tp30) cc_final: 0.8162 (tp30) REVERT: I 224 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8573 (mmtp) REVERT: J 147 LEU cc_start: 0.8425 (tp) cc_final: 0.8128 (pp) REVERT: J 224 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8678 (mtpp) REVERT: J 245 MET cc_start: 0.8778 (mmm) cc_final: 0.8492 (mmm) outliers start: 15 outliers final: 9 residues processed: 176 average time/residue: 1.8365 time to fit residues: 349.4584 Evaluate side-chains 163 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.057473 restraints weight = 25661.267| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.95 r_work: 0.2590 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 17090 Z= 0.304 Angle : 0.552 6.187 23090 Z= 0.298 Chirality : 0.046 0.128 2720 Planarity : 0.004 0.035 2970 Dihedral : 4.331 15.371 2399 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.39 % Allowed : 19.32 % Favored : 77.29 % 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: 1.79 (0.18), residues: 2240 helix: 1.77 (0.18), residues: 830 sheet: 0.98 (0.18), residues: 790 loop : 0.88 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 94 HIS 0.001 0.000 HIS J 208 PHE 0.012 0.003 PHE C 225 TYR 0.009 0.002 TYR G 210 ARG 0.002 0.001 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 731) hydrogen bonds : angle 4.25398 ( 2073) covalent geometry : bond 0.00694 (17090) covalent geometry : angle 0.55176 (23090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 1.841 Fit side-chains REVERT: A 109 GLU cc_start: 0.8429 (tp30) cc_final: 0.8095 (tp30) REVERT: A 115 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 143 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7274 (tm) REVERT: A 224 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8535 (mttp) REVERT: B 109 GLU cc_start: 0.8429 (tp30) cc_final: 0.8094 (tp30) REVERT: B 115 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7339 (p0) REVERT: B 143 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7357 (tm) REVERT: B 224 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8429 (mttm) REVERT: C 109 GLU cc_start: 0.8396 (tp30) cc_final: 0.8014 (tp30) REVERT: C 115 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7379 (p0) REVERT: C 143 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7454 (tm) REVERT: C 224 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8471 (mmtp) REVERT: D 143 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7424 (tm) REVERT: D 224 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8481 (mmtp) REVERT: E 109 GLU cc_start: 0.8494 (tp30) cc_final: 0.8227 (tp30) REVERT: E 143 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7415 (tm) REVERT: E 224 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8493 (mtpp) REVERT: F 109 GLU cc_start: 0.8457 (tp30) cc_final: 0.8130 (tp30) REVERT: F 115 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7342 (p0) REVERT: F 143 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7298 (tm) REVERT: F 224 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8502 (mttp) REVERT: G 143 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7317 (tm) REVERT: G 224 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8429 (mttp) REVERT: H 143 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7433 (tm) REVERT: H 224 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8517 (mtpp) REVERT: I 109 GLU cc_start: 0.8488 (tp30) cc_final: 0.8286 (tp30) REVERT: I 143 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7427 (tm) REVERT: I 224 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8477 (mmtp) REVERT: J 143 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7322 (tm) REVERT: J 224 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8507 (mttp) outliers start: 60 outliers final: 9 residues processed: 201 average time/residue: 1.8750 time to fit residues: 406.6414 Evaluate side-chains 173 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.057363 restraints weight = 25484.625| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.95 r_work: 0.2588 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 17090 Z= 0.258 Angle : 0.502 5.791 23090 Z= 0.271 Chirality : 0.044 0.125 2720 Planarity : 0.003 0.026 2970 Dihedral : 4.288 15.291 2390 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.03 % Allowed : 17.91 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.18), residues: 2240 helix: 2.11 (0.18), residues: 830 sheet: 0.65 (0.18), residues: 830 loop : 0.88 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 94 HIS 0.001 0.000 HIS J 208 PHE 0.010 0.003 PHE C 225 TYR 0.007 0.001 TYR G 210 ARG 0.003 0.001 ARG J 190 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 731) hydrogen bonds : angle 4.05724 ( 2073) covalent geometry : bond 0.00582 (17090) covalent geometry : angle 0.50167 (23090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 2.360 Fit side-chains REVERT: A 109 GLU cc_start: 0.8506 (tp30) cc_final: 0.8200 (tp30) REVERT: A 143 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7214 (tm) REVERT: A 224 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8521 (mttp) REVERT: B 109 GLU cc_start: 0.8514 (tp30) cc_final: 0.8248 (tp30) REVERT: B 115 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7436 (p0) REVERT: B 143 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7374 (tm) REVERT: B 224 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8405 (mttp) REVERT: C 143 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7420 (tm) REVERT: C 224 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8499 (mttp) REVERT: C 238 LYS cc_start: 0.9101 (mtpm) cc_final: 0.8854 (tppp) REVERT: D 143 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7256 (tm) REVERT: D 224 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8484 (mmtp) REVERT: E 143 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7397 (tm) REVERT: E 224 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8466 (mttp) REVERT: F 109 GLU cc_start: 0.8522 (tp30) cc_final: 0.8220 (tp30) REVERT: F 143 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7248 (tm) REVERT: F 224 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8495 (mttp) REVERT: G 109 GLU cc_start: 0.8381 (tp30) cc_final: 0.8180 (tp30) REVERT: G 143 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7328 (tm) REVERT: G 224 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8411 (mttp) REVERT: H 109 GLU cc_start: 0.8376 (tp30) cc_final: 0.8145 (tp30) REVERT: H 143 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7432 (tm) REVERT: H 224 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8518 (mtpp) REVERT: I 143 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7211 (tm) REVERT: I 224 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8468 (mmtp) REVERT: J 109 GLU cc_start: 0.8500 (tp30) cc_final: 0.7984 (mm-30) REVERT: J 224 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8479 (mttp) outliers start: 36 outliers final: 11 residues processed: 182 average time/residue: 1.7959 time to fit residues: 353.8410 Evaluate side-chains 176 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 179 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.057097 restraints weight = 25900.341| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 1.95 r_work: 0.2578 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 17090 Z= 0.279 Angle : 0.511 6.084 23090 Z= 0.275 Chirality : 0.045 0.125 2720 Planarity : 0.003 0.029 2970 Dihedral : 4.361 15.695 2390 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.32 % Allowed : 17.29 % Favored : 80.40 % 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: 1.77 (0.18), residues: 2240 helix: 2.24 (0.18), residues: 830 sheet: 0.53 (0.18), residues: 830 loop : 0.77 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 113 HIS 0.001 0.000 HIS E 208 PHE 0.010 0.003 PHE C 225 TYR 0.007 0.001 TYR G 210 ARG 0.003 0.001 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 731) hydrogen bonds : angle 3.99315 ( 2073) covalent geometry : bond 0.00631 (17090) covalent geometry : angle 0.51073 (23090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.863 Fit side-chains REVERT: A 109 GLU cc_start: 0.8488 (tp30) cc_final: 0.8198 (tp30) REVERT: A 143 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7225 (tm) REVERT: A 224 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8507 (mttp) REVERT: B 109 GLU cc_start: 0.8571 (tp30) cc_final: 0.8351 (tp30) REVERT: B 143 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7385 (tm) REVERT: B 224 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8408 (mttp) REVERT: C 143 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7419 (tm) REVERT: C 224 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8520 (mtpp) REVERT: D 109 GLU cc_start: 0.8529 (tp30) cc_final: 0.8252 (tp30) REVERT: D 115 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7457 (p0) REVERT: D 143 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7211 (tm) REVERT: D 224 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8506 (mmtp) REVERT: E 109 GLU cc_start: 0.8457 (tp30) cc_final: 0.8154 (tp30) REVERT: E 115 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7482 (p0) REVERT: E 143 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7384 (tm) REVERT: E 224 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8459 (mttp) REVERT: F 109 GLU cc_start: 0.8491 (tp30) cc_final: 0.8198 (tp30) REVERT: F 143 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7292 (tm) REVERT: F 224 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8493 (mttp) REVERT: G 109 GLU cc_start: 0.8419 (tp30) cc_final: 0.8198 (tp30) REVERT: G 115 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7320 (p0) REVERT: G 143 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7349 (tm) REVERT: G 224 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8412 (mttp) REVERT: H 143 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7475 (tm) REVERT: H 224 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8521 (mtpp) REVERT: I 109 GLU cc_start: 0.8495 (tp30) cc_final: 0.8230 (tp30) REVERT: I 143 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7232 (tm) REVERT: I 224 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8496 (mmtp) REVERT: J 109 GLU cc_start: 0.8494 (tp30) cc_final: 0.7932 (mm-30) REVERT: J 143 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7303 (tm) REVERT: J 224 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8472 (mttp) outliers start: 41 outliers final: 11 residues processed: 187 average time/residue: 1.7690 time to fit residues: 359.5331 Evaluate side-chains 180 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 6 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.058885 restraints weight = 25841.516| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.95 r_work: 0.2627 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 17090 Z= 0.127 Angle : 0.406 4.951 23090 Z= 0.222 Chirality : 0.041 0.120 2720 Planarity : 0.002 0.022 2970 Dihedral : 3.930 14.587 2390 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.92 % Allowed : 17.40 % Favored : 80.68 % 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: 1.93 (0.18), residues: 2240 helix: 2.47 (0.19), residues: 830 sheet: 0.67 (0.18), residues: 820 loop : 0.61 (0.28), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 113 HIS 0.001 0.000 HIS J 208 PHE 0.006 0.002 PHE H 55 TYR 0.006 0.001 TYR J 134 ARG 0.003 0.000 ARG D 116 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 731) hydrogen bonds : angle 3.77657 ( 2073) covalent geometry : bond 0.00271 (17090) covalent geometry : angle 0.40570 (23090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 2.091 Fit side-chains REVERT: A 109 GLU cc_start: 0.8478 (tp30) cc_final: 0.8057 (tp30) REVERT: A 115 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7233 (p0) REVERT: A 143 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7306 (tm) REVERT: A 224 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8461 (mttp) REVERT: A 238 LYS cc_start: 0.9064 (mtpm) cc_final: 0.8839 (tppp) REVERT: B 143 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7420 (tm) REVERT: B 224 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8415 (mttm) REVERT: C 109 GLU cc_start: 0.8394 (tp30) cc_final: 0.8152 (tp30) REVERT: C 143 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7474 (tm) REVERT: C 224 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8503 (mttp) REVERT: D 109 GLU cc_start: 0.8580 (tp30) cc_final: 0.8278 (tp30) REVERT: D 115 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7409 (p0) REVERT: D 143 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7262 (tm) REVERT: D 224 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8491 (mmtp) REVERT: E 109 GLU cc_start: 0.8496 (tp30) cc_final: 0.8222 (tp30) REVERT: E 143 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7407 (tm) REVERT: E 224 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8436 (mttp) REVERT: F 109 GLU cc_start: 0.8478 (tp30) cc_final: 0.8055 (tp30) REVERT: F 115 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7289 (p0) REVERT: F 143 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7339 (tm) REVERT: F 224 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8461 (mttp) REVERT: F 238 LYS cc_start: 0.9055 (mtpm) cc_final: 0.8829 (tppp) REVERT: G 115 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7353 (p0) REVERT: G 143 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7390 (tm) REVERT: G 224 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8424 (mttm) REVERT: H 109 GLU cc_start: 0.8355 (tp30) cc_final: 0.8146 (tp30) REVERT: H 143 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7478 (tm) REVERT: H 224 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8502 (mttp) REVERT: I 109 GLU cc_start: 0.8454 (tp30) cc_final: 0.8155 (tp30) REVERT: I 143 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7265 (tm) REVERT: I 224 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8495 (mmtp) REVERT: J 109 GLU cc_start: 0.8465 (tp30) cc_final: 0.7847 (mm-30) REVERT: J 143 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7349 (tm) REVERT: J 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8445 (mttp) outliers start: 34 outliers final: 13 residues processed: 187 average time/residue: 1.8030 time to fit residues: 365.9690 Evaluate side-chains 184 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 44 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.056781 restraints weight = 25938.051| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 1.95 r_work: 0.2574 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 17090 Z= 0.324 Angle : 0.528 6.444 23090 Z= 0.285 Chirality : 0.046 0.128 2720 Planarity : 0.003 0.038 2970 Dihedral : 4.399 16.022 2390 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.15 % Allowed : 16.50 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 2240 helix: 3.06 (0.18), residues: 760 sheet: 0.40 (0.17), residues: 860 loop : 1.34 (0.29), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 94 HIS 0.001 0.000 HIS J 208 PHE 0.011 0.003 PHE C 225 TYR 0.007 0.001 TYR B 210 ARG 0.002 0.001 ARG G 108 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 731) hydrogen bonds : angle 3.94045 ( 2073) covalent geometry : bond 0.00736 (17090) covalent geometry : angle 0.52821 (23090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 2.134 Fit side-chains REVERT: A 109 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: A 115 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 143 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7256 (tm) REVERT: A 224 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8505 (mttp) REVERT: B 143 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7330 (tm) REVERT: B 224 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8420 (mttp) REVERT: C 143 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7355 (tm) REVERT: C 224 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8538 (mtpp) REVERT: D 109 GLU cc_start: 0.8613 (tp30) cc_final: 0.8301 (tp30) REVERT: D 115 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7572 (p0) REVERT: D 143 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7188 (tm) REVERT: D 224 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8515 (mmtp) REVERT: E 143 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7324 (tm) REVERT: E 224 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8483 (mttp) REVERT: F 109 GLU cc_start: 0.8549 (tp30) cc_final: 0.8266 (tp30) REVERT: F 115 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7561 (p0) REVERT: F 143 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7254 (tm) REVERT: F 224 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8499 (mttp) REVERT: G 143 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7304 (tm) REVERT: G 224 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8429 (mttp) REVERT: H 143 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7368 (tm) REVERT: H 224 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8549 (mtpp) REVERT: I 109 GLU cc_start: 0.8524 (tp30) cc_final: 0.8245 (tp30) REVERT: I 143 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7199 (tm) REVERT: I 224 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8509 (mmtp) REVERT: J 109 GLU cc_start: 0.8507 (tp30) cc_final: 0.7927 (mm-30) REVERT: J 143 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7302 (tm) REVERT: J 224 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8486 (mttp) outliers start: 38 outliers final: 14 residues processed: 184 average time/residue: 1.7993 time to fit residues: 359.3359 Evaluate side-chains 185 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 141 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.057875 restraints weight = 25508.351| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.93 r_work: 0.2601 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 17090 Z= 0.200 Angle : 0.451 5.113 23090 Z= 0.246 Chirality : 0.043 0.122 2720 Planarity : 0.002 0.023 2970 Dihedral : 4.197 15.285 2390 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.81 % Allowed : 16.72 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 2240 helix: 3.15 (0.18), residues: 760 sheet: 0.53 (0.17), residues: 840 loop : 1.10 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.001 0.000 HIS E 208 PHE 0.008 0.002 PHE C 225 TYR 0.006 0.001 TYR B 93 ARG 0.002 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 731) hydrogen bonds : angle 3.84623 ( 2073) covalent geometry : bond 0.00444 (17090) covalent geometry : angle 0.45106 (23090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.951 Fit side-chains REVERT: A 109 GLU cc_start: 0.8571 (tp30) cc_final: 0.8166 (tp30) REVERT: A 115 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7514 (p0) REVERT: A 143 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7316 (tm) REVERT: A 224 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8483 (mttp) REVERT: B 143 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7328 (tm) REVERT: B 224 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8403 (mttp) REVERT: C 143 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7381 (tm) REVERT: C 224 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8503 (mtpp) REVERT: D 109 GLU cc_start: 0.8620 (tp30) cc_final: 0.8121 (mm-30) REVERT: D 115 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7296 (p0) REVERT: D 143 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7203 (tm) REVERT: D 224 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8507 (mmtp) REVERT: E 109 GLU cc_start: 0.8387 (tp30) cc_final: 0.8161 (tp30) REVERT: E 143 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7324 (tm) REVERT: E 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8437 (mttp) REVERT: F 109 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: F 115 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7528 (p0) REVERT: F 143 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7281 (tm) REVERT: F 224 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8469 (mttp) REVERT: G 143 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7322 (tm) REVERT: G 224 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8403 (mttp) REVERT: H 109 GLU cc_start: 0.8458 (tp30) cc_final: 0.8241 (tp30) REVERT: H 143 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7413 (tm) REVERT: H 224 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8516 (mtpp) REVERT: I 109 GLU cc_start: 0.8559 (tp30) cc_final: 0.8256 (tp30) REVERT: I 143 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7212 (tm) REVERT: I 224 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8497 (mmtp) REVERT: J 109 GLU cc_start: 0.8499 (tp30) cc_final: 0.7900 (mm-30) REVERT: J 143 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7323 (tm) REVERT: J 224 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8449 (mttp) outliers start: 32 outliers final: 15 residues processed: 182 average time/residue: 1.7556 time to fit residues: 346.9815 Evaluate side-chains 187 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 117 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN I 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.058193 restraints weight = 25626.264| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.94 r_work: 0.2609 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 17090 Z= 0.174 Angle : 0.434 5.013 23090 Z= 0.237 Chirality : 0.042 0.121 2720 Planarity : 0.002 0.019 2970 Dihedral : 4.105 15.049 2390 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.81 % Allowed : 16.78 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.19), residues: 2240 helix: 3.20 (0.19), residues: 760 sheet: 0.56 (0.18), residues: 840 loop : 1.05 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 113 HIS 0.001 0.000 HIS H 208 PHE 0.007 0.002 PHE C 225 TYR 0.007 0.001 TYR F 93 ARG 0.002 0.000 ARG J 190 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 731) hydrogen bonds : angle 3.80754 ( 2073) covalent geometry : bond 0.00385 (17090) covalent geometry : angle 0.43361 (23090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.912 Fit side-chains REVERT: A 109 GLU cc_start: 0.8576 (tp30) cc_final: 0.8175 (tp30) REVERT: A 115 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7586 (p0) REVERT: A 143 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7363 (tm) REVERT: A 224 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8495 (mttp) REVERT: B 143 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7321 (tm) REVERT: B 224 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8406 (mttm) REVERT: C 109 GLU cc_start: 0.8385 (tp30) cc_final: 0.8140 (mm-30) REVERT: C 115 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7428 (p0) REVERT: C 143 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7445 (tm) REVERT: C 224 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8498 (mtpp) REVERT: D 109 GLU cc_start: 0.8632 (tp30) cc_final: 0.8138 (mm-30) REVERT: D 115 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7321 (p0) REVERT: D 143 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7208 (tm) REVERT: D 224 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8505 (mmtp) REVERT: E 109 GLU cc_start: 0.8447 (tp30) cc_final: 0.8226 (tp30) REVERT: E 143 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7371 (tm) REVERT: E 224 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8434 (mttp) REVERT: F 109 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: F 115 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7589 (p0) REVERT: F 143 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7373 (tm) REVERT: F 224 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8466 (mttp) REVERT: G 109 GLU cc_start: 0.8407 (tp30) cc_final: 0.8035 (mm-30) REVERT: G 115 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7241 (p0) REVERT: G 143 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7348 (tm) REVERT: G 224 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8402 (mttm) REVERT: H 109 GLU cc_start: 0.8490 (tp30) cc_final: 0.8265 (tp30) REVERT: H 143 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7421 (tm) REVERT: H 224 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8499 (mtpp) REVERT: I 109 GLU cc_start: 0.8577 (tp30) cc_final: 0.8276 (tp30) REVERT: I 143 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7219 (tm) REVERT: I 224 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8491 (mmtp) REVERT: J 109 GLU cc_start: 0.8492 (tp30) cc_final: 0.7892 (mm-30) REVERT: J 143 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7336 (tm) REVERT: J 224 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8446 (mttp) outliers start: 32 outliers final: 13 residues processed: 184 average time/residue: 1.7610 time to fit residues: 351.1836 Evaluate side-chains 188 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 45 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 172 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN E 115 ASN G 115 ASN I 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.059447 restraints weight = 25844.091| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.96 r_work: 0.2642 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 17090 Z= 0.099 Angle : 0.386 4.886 23090 Z= 0.213 Chirality : 0.041 0.120 2720 Planarity : 0.002 0.012 2970 Dihedral : 3.778 14.316 2390 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.69 % Allowed : 16.84 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 2240 helix: 3.27 (0.19), residues: 760 sheet: 0.65 (0.18), residues: 840 loop : 1.05 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 113 HIS 0.001 0.000 HIS F 208 PHE 0.005 0.001 PHE B 55 TYR 0.006 0.001 TYR J 134 ARG 0.002 0.000 ARG J 190 Details of bonding type rmsd hydrogen bonds : bond 0.02559 ( 731) hydrogen bonds : angle 3.68662 ( 2073) covalent geometry : bond 0.00202 (17090) covalent geometry : angle 0.38579 (23090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.989 Fit side-chains REVERT: A 109 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: A 143 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7324 (tm) REVERT: A 224 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8462 (mttp) REVERT: A 238 LYS cc_start: 0.9059 (mtpm) cc_final: 0.8822 (tppp) REVERT: B 143 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7278 (tm) REVERT: B 224 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8405 (mttm) REVERT: C 109 GLU cc_start: 0.8405 (tp30) cc_final: 0.8115 (mm-30) REVERT: C 115 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7374 (p0) REVERT: C 143 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7435 (tm) REVERT: C 224 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8484 (mtpp) REVERT: D 109 GLU cc_start: 0.8609 (tp30) cc_final: 0.8020 (mm-30) REVERT: D 143 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7198 (tm) REVERT: D 224 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8458 (mmtp) REVERT: E 109 GLU cc_start: 0.8444 (tp30) cc_final: 0.7878 (mm-30) REVERT: E 143 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7404 (tm) REVERT: E 224 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8409 (mttp) REVERT: E 238 LYS cc_start: 0.9088 (mtpm) cc_final: 0.8830 (tppp) REVERT: F 109 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: F 143 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7325 (tm) REVERT: F 224 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8445 (mttp) REVERT: F 238 LYS cc_start: 0.9057 (mtpm) cc_final: 0.8820 (tppp) REVERT: G 109 GLU cc_start: 0.8409 (tp30) cc_final: 0.8051 (mm-30) REVERT: G 115 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7308 (p0) REVERT: G 143 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7308 (tm) REVERT: G 224 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8413 (mttm) REVERT: H 109 GLU cc_start: 0.8426 (tp30) cc_final: 0.8194 (tp30) REVERT: H 143 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7448 (tm) REVERT: H 224 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8495 (mttp) REVERT: H 238 LYS cc_start: 0.9079 (mtpm) cc_final: 0.8832 (tppp) REVERT: I 109 GLU cc_start: 0.8580 (tp30) cc_final: 0.8127 (mm-30) REVERT: I 143 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7206 (tm) REVERT: I 224 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8453 (mmtp) REVERT: J 109 GLU cc_start: 0.8500 (tp30) cc_final: 0.7920 (mm-30) REVERT: J 143 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7393 (tm) REVERT: J 224 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8420 (mttp) outliers start: 30 outliers final: 9 residues processed: 183 average time/residue: 1.8815 time to fit residues: 372.6378 Evaluate side-chains 182 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 36 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 176 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN E 115 ASN F 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.058090 restraints weight = 25612.182| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.94 r_work: 0.2608 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 17090 Z= 0.191 Angle : 0.440 5.045 23090 Z= 0.239 Chirality : 0.042 0.121 2720 Planarity : 0.002 0.035 2970 Dihedral : 4.043 14.863 2390 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.75 % Allowed : 17.06 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2240 helix: 3.23 (0.19), residues: 760 sheet: 0.63 (0.18), residues: 840 loop : 1.06 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 113 HIS 0.001 0.000 HIS A 208 PHE 0.008 0.002 PHE C 225 TYR 0.007 0.001 TYR B 93 ARG 0.008 0.000 ARG G 190 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 731) hydrogen bonds : angle 3.77539 ( 2073) covalent geometry : bond 0.00426 (17090) covalent geometry : angle 0.43994 (23090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 2.159 Fit side-chains REVERT: A 109 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: A 143 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7339 (tm) REVERT: A 224 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8480 (mttp) REVERT: B 143 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7278 (tm) REVERT: B 224 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8384 (mttm) REVERT: C 109 GLU cc_start: 0.8430 (tp30) cc_final: 0.8149 (mm-30) REVERT: C 115 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7369 (p0) REVERT: C 143 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7368 (tm) REVERT: C 224 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8490 (mtpp) REVERT: D 109 GLU cc_start: 0.8596 (tp30) cc_final: 0.8110 (mm-30) REVERT: D 143 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7175 (tm) REVERT: D 224 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8472 (mmtp) REVERT: E 109 GLU cc_start: 0.8508 (tp30) cc_final: 0.7969 (mm-30) REVERT: E 143 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7380 (tm) REVERT: E 224 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8432 (mttp) REVERT: E 238 LYS cc_start: 0.9096 (mtpm) cc_final: 0.8828 (tppp) REVERT: F 109 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8196 (tp30) REVERT: F 143 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7307 (tm) REVERT: F 224 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8468 (mttp) REVERT: G 109 GLU cc_start: 0.8445 (tp30) cc_final: 0.7943 (mm-30) REVERT: G 115 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7452 (p0) REVERT: G 143 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7258 (tm) REVERT: G 224 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8393 (mttm) REVERT: H 109 GLU cc_start: 0.8466 (tp30) cc_final: 0.8229 (tp30) REVERT: H 143 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7361 (tm) REVERT: H 224 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8485 (mtpp) REVERT: I 109 GLU cc_start: 0.8618 (tp30) cc_final: 0.8174 (mm-30) REVERT: I 115 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7315 (p0) REVERT: I 143 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7177 (tm) REVERT: I 224 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8463 (mmtp) REVERT: J 109 GLU cc_start: 0.8511 (tp30) cc_final: 0.7913 (mm-30) REVERT: J 143 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7335 (tm) REVERT: J 224 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8429 (mttp) REVERT: J 238 LYS cc_start: 0.9093 (mtpm) cc_final: 0.8819 (tppp) outliers start: 31 outliers final: 14 residues processed: 184 average time/residue: 1.8098 time to fit residues: 361.8406 Evaluate side-chains 188 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.059135 restraints weight = 25507.239| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.94 r_work: 0.2634 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 17090 Z= 0.114 Angle : 0.398 4.907 23090 Z= 0.218 Chirality : 0.041 0.120 2720 Planarity : 0.002 0.033 2970 Dihedral : 3.829 14.448 2390 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.64 % Allowed : 17.23 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 2240 helix: 3.29 (0.19), residues: 760 sheet: 0.69 (0.18), residues: 840 loop : 1.04 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 113 HIS 0.001 0.000 HIS H 208 PHE 0.005 0.002 PHE B 55 TYR 0.006 0.001 TYR B 93 ARG 0.008 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.02592 ( 731) hydrogen bonds : angle 3.70105 ( 2073) covalent geometry : bond 0.00242 (17090) covalent geometry : angle 0.39769 (23090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18175.19 seconds wall clock time: 314 minutes 43.49 seconds (18883.49 seconds total)