Starting phenix.real_space_refine on Sun Jun 15 02:25:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2v_47469/06_2025/9e2v_47469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2v_47469/06_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_47469/06_2025/9e2v_47469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2v_47469/06_2025/9e2v_47469.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2v_47469/06_2025/9e2v_47469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2v_47469/06_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-5710/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: 8.20, per 1000 atoms: 0.48 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: 4.71 Conformation dependent library (CDL) restraints added in 2.6 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: 1.48 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: 4.73 Time building geometry restraints manager: 5.52 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: 0.17 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: 9.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.570 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:14.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.830 ------------------------------------------------------------------------------- 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 : 1.938 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: 1.9001 time to fit residues: 362.0767 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 : 2.013 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.057471 restraints weight = 25661.267| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.95 r_work: 0.2587 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: 0.9167 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 : 2.034 Fit side-chains REVERT: A 109 GLU cc_start: 0.8428 (tp30) cc_final: 0.8094 (tp30) REVERT: A 115 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7315 (p0) REVERT: A 143 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7266 (tm) REVERT: A 224 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8536 (mttp) REVERT: B 109 GLU cc_start: 0.8429 (tp30) cc_final: 0.8095 (tp30) REVERT: B 115 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7337 (p0) REVERT: B 143 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7351 (tm) REVERT: B 224 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8430 (mttm) REVERT: C 109 GLU cc_start: 0.8395 (tp30) cc_final: 0.8013 (tp30) REVERT: C 115 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7374 (p0) REVERT: C 143 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7448 (tm) REVERT: C 224 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8473 (mmtp) REVERT: D 143 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7421 (tm) REVERT: D 224 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8483 (mmtp) REVERT: E 109 GLU cc_start: 0.8493 (tp30) cc_final: 0.8225 (tp30) REVERT: E 143 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7408 (tm) REVERT: E 224 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8493 (mtpp) REVERT: F 109 GLU cc_start: 0.8456 (tp30) cc_final: 0.8129 (tp30) REVERT: F 115 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7339 (p0) REVERT: F 143 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7291 (tm) REVERT: F 224 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8505 (mttp) REVERT: G 143 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7313 (tm) REVERT: G 224 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8430 (mttp) REVERT: H 143 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7425 (tm) REVERT: H 224 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8518 (mtpp) REVERT: I 109 GLU cc_start: 0.8486 (tp30) cc_final: 0.8283 (tp30) REVERT: I 143 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7426 (tm) REVERT: I 224 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8480 (mmtp) REVERT: J 143 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7315 (tm) REVERT: J 224 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8506 (mttp) outliers start: 60 outliers final: 9 residues processed: 201 average time/residue: 1.8443 time to fit residues: 400.4545 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 : 1.817 ------------------------------------------------------------------------------- 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: 10.0000 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: 5.9990 chunk 95 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.090419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.057479 restraints weight = 25477.525| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 1.95 r_work: 0.2588 rms_B_bonded: 2.33 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: 0.9167 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 17090 Z= 0.248 Angle : 0.494 5.774 23090 Z= 0.267 Chirality : 0.044 0.125 2720 Planarity : 0.003 0.025 2970 Dihedral : 4.264 15.231 2390 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.09 % Allowed : 17.80 % Favored : 80.11 % 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: 1.81 (0.18), residues: 2240 helix: 2.13 (0.18), residues: 830 sheet: 0.66 (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 D 94 HIS 0.000 0.000 HIS E 208 PHE 0.010 0.003 PHE C 225 TYR 0.007 0.001 TYR A 93 ARG 0.003 0.001 ARG J 190 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 731) hydrogen bonds : angle 4.05252 ( 2073) covalent geometry : bond 0.00558 (17090) covalent geometry : angle 0.49393 (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 193 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 2.016 Fit side-chains REVERT: A 109 GLU cc_start: 0.8510 (tp30) cc_final: 0.8193 (tp30) REVERT: A 143 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7236 (tm) REVERT: A 224 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8517 (mttp) REVERT: B 109 GLU cc_start: 0.8521 (tp30) cc_final: 0.8247 (tp30) REVERT: B 115 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7401 (p0) REVERT: B 143 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7353 (tm) REVERT: B 224 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8399 (mttm) REVERT: C 143 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7403 (tm) REVERT: C 224 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8493 (mttp) REVERT: C 238 LYS cc_start: 0.9093 (mtpm) cc_final: 0.8847 (tppp) REVERT: D 143 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7231 (tm) REVERT: D 224 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8484 (mmtp) REVERT: E 143 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7383 (tm) REVERT: E 224 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8462 (mttp) REVERT: F 109 GLU cc_start: 0.8527 (tp30) cc_final: 0.8214 (tp30) REVERT: F 143 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7230 (tm) REVERT: F 224 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8489 (mttp) REVERT: G 109 GLU cc_start: 0.8385 (tp30) cc_final: 0.8183 (tp30) REVERT: G 143 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7304 (tm) REVERT: G 224 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8405 (mttm) REVERT: H 109 GLU cc_start: 0.8372 (tp30) cc_final: 0.8139 (tp30) REVERT: H 143 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7413 (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: 0.7429 (tm) REVERT: I 224 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8462 (mmtp) REVERT: J 109 GLU cc_start: 0.8504 (tp30) cc_final: 0.7988 (mm-30) REVERT: J 224 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8473 (mttp) outliers start: 37 outliers final: 9 residues processed: 183 average time/residue: 1.7822 time to fit residues: 353.7641 Evaluate side-chains 173 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 143 LEU 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: 0.9980 chunk 160 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.089497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057026 restraints weight = 25875.285| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.94 r_work: 0.2574 rms_B_bonded: 2.32 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: 0.9178 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 17090 Z= 0.304 Angle : 0.525 6.312 23090 Z= 0.283 Chirality : 0.046 0.125 2720 Planarity : 0.003 0.033 2970 Dihedral : 4.399 15.812 2390 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.09 % Allowed : 17.40 % Favored : 80.51 % 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: 1.73 (0.18), residues: 2240 helix: 2.22 (0.18), residues: 830 sheet: 0.38 (0.17), residues: 850 loop : 1.01 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 94 HIS 0.001 0.000 HIS F 208 PHE 0.011 0.003 PHE C 225 TYR 0.007 0.001 TYR B 210 ARG 0.003 0.001 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 731) hydrogen bonds : angle 4.01331 ( 2073) covalent geometry : bond 0.00689 (17090) covalent geometry : angle 0.52491 (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 195 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.857 Fit side-chains REVERT: A 109 GLU cc_start: 0.8498 (tp30) cc_final: 0.8211 (tp30) REVERT: A 143 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7213 (tm) REVERT: A 224 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8507 (mttp) REVERT: B 109 GLU cc_start: 0.8569 (tp30) cc_final: 0.8344 (tp30) REVERT: B 143 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7371 (tm) REVERT: B 224 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8412 (mttp) REVERT: C 143 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7413 (tm) REVERT: C 224 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8519 (mtpp) REVERT: D 143 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7172 (tm) REVERT: D 224 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8506 (mmtp) REVERT: E 109 GLU cc_start: 0.8443 (tp30) cc_final: 0.8135 (tp30) REVERT: E 115 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7488 (p0) REVERT: E 143 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7358 (tm) REVERT: E 224 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8462 (mttp) REVERT: F 109 GLU cc_start: 0.8493 (tp30) cc_final: 0.8199 (tp30) REVERT: F 143 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7270 (tm) REVERT: F 224 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8503 (mttp) REVERT: G 109 GLU cc_start: 0.8428 (tp30) cc_final: 0.8209 (tp30) REVERT: G 143 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7337 (tm) REVERT: G 224 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8415 (mttp) REVERT: H 143 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7462 (tm) REVERT: H 224 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8520 (mtpp) REVERT: I 109 GLU cc_start: 0.8500 (tp30) cc_final: 0.8240 (tp30) REVERT: I 143 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7325 (tm) REVERT: I 224 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8494 (mmtp) REVERT: J 109 GLU cc_start: 0.8500 (tp30) cc_final: 0.7933 (mm-30) REVERT: J 143 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7309 (tm) REVERT: J 224 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8474 (mttp) outliers start: 37 outliers final: 12 residues processed: 186 average time/residue: 1.7094 time to fit residues: 345.3887 Evaluate side-chains 179 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.093348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.061074 restraints weight = 25586.970| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.93 r_work: 0.2642 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 17090 Z= 0.123 Angle : 0.407 4.946 23090 Z= 0.223 Chirality : 0.041 0.121 2720 Planarity : 0.002 0.014 2970 Dihedral : 3.944 14.673 2390 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.86 % Allowed : 17.46 % 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: 2.37 (0.19), residues: 2240 helix: 3.16 (0.18), residues: 760 sheet: 0.64 (0.18), residues: 840 loop : 1.07 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 113 HIS 0.001 0.000 HIS A 208 PHE 0.006 0.002 PHE E 55 TYR 0.006 0.001 TYR A 134 ARG 0.002 0.000 ARG J 190 Details of bonding type rmsd hydrogen bonds : bond 0.02871 ( 731) hydrogen bonds : angle 3.78654 ( 2073) covalent geometry : bond 0.00261 (17090) covalent geometry : angle 0.40715 (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 191 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.915 Fit side-chains REVERT: A 109 GLU cc_start: 0.8474 (tp30) cc_final: 0.8051 (tp30) REVERT: A 115 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7244 (p0) REVERT: A 143 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7276 (tm) REVERT: A 224 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8465 (mttp) REVERT: B 143 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7406 (tm) REVERT: B 224 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8440 (mttm) REVERT: C 109 GLU cc_start: 0.8470 (tp30) cc_final: 0.8257 (tp30) REVERT: C 143 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7442 (tm) REVERT: C 224 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8502 (mttp) REVERT: D 109 GLU cc_start: 0.8555 (tp30) cc_final: 0.8301 (tp30) REVERT: D 143 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7275 (tm) REVERT: D 224 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8502 (mmtp) REVERT: E 109 GLU cc_start: 0.8524 (tp30) cc_final: 0.8192 (tp30) REVERT: E 115 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7451 (p0) REVERT: E 143 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7387 (tm) REVERT: E 224 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8427 (mttp) REVERT: F 109 GLU cc_start: 0.8486 (tp30) cc_final: 0.8067 (tp30) REVERT: F 115 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7306 (p0) REVERT: F 143 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7312 (tm) REVERT: F 224 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8456 (mttp) REVERT: G 109 GLU cc_start: 0.8392 (tp30) cc_final: 0.8150 (tp30) REVERT: G 115 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7203 (p0) REVERT: G 143 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7361 (tm) REVERT: G 224 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8454 (mttm) REVERT: H 143 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7468 (tm) REVERT: H 224 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8518 (mtpp) REVERT: I 109 GLU cc_start: 0.8536 (tp30) cc_final: 0.8275 (tp30) REVERT: I 143 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7409 (tm) REVERT: I 224 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8505 (mmtp) REVERT: J 109 GLU cc_start: 0.8459 (tp30) cc_final: 0.7838 (mm-30) REVERT: J 143 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7329 (tm) REVERT: J 224 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8435 (mttp) outliers start: 33 outliers final: 11 residues processed: 186 average time/residue: 1.7384 time to fit residues: 351.0874 Evaluate side-chains 183 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.088904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.056252 restraints weight = 26024.238| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 1.95 r_work: 0.2564 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.041 17090 Z= 0.407 Angle : 0.581 7.075 23090 Z= 0.313 Chirality : 0.049 0.144 2720 Planarity : 0.004 0.049 2970 Dihedral : 4.543 16.426 2390 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.26 % Allowed : 16.16 % Favored : 81.58 % 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: 1.67 (0.19), residues: 2240 helix: 2.28 (0.19), residues: 830 sheet: 0.26 (0.17), residues: 850 loop : 0.95 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 94 HIS 0.001 0.000 HIS E 208 PHE 0.013 0.004 PHE C 225 TYR 0.008 0.002 TYR G 210 ARG 0.003 0.001 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 731) hydrogen bonds : angle 4.00496 ( 2073) covalent geometry : bond 0.00929 (17090) covalent geometry : angle 0.58076 (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 196 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.888 Fit side-chains REVERT: A 109 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: A 115 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 143 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7247 (tm) REVERT: A 224 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8517 (mttp) REVERT: B 143 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7279 (tm) REVERT: B 224 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8434 (mttp) REVERT: C 109 GLU cc_start: 0.8455 (tp30) cc_final: 0.8220 (tp30) REVERT: C 143 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7333 (tm) REVERT: C 224 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8560 (mtpp) REVERT: D 109 GLU cc_start: 0.8549 (tp30) cc_final: 0.8311 (tp30) REVERT: D 143 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7116 (tm) REVERT: D 224 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8590 (mttm) REVERT: E 143 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7267 (tm) REVERT: E 224 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8488 (mttp) REVERT: F 109 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: F 115 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7670 (p0) REVERT: F 143 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7252 (tm) REVERT: F 224 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8495 (mttp) REVERT: G 143 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7291 (tm) REVERT: G 224 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8433 (mttp) REVERT: H 109 GLU cc_start: 0.8437 (tp30) cc_final: 0.8225 (tp30) REVERT: H 143 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7364 (tm) REVERT: H 224 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8557 (mtpp) REVERT: I 109 GLU cc_start: 0.8568 (tp30) cc_final: 0.8285 (tp30) REVERT: I 143 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7215 (tm) REVERT: I 224 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8515 (mmtp) REVERT: J 109 GLU cc_start: 0.8517 (tp30) cc_final: 0.7939 (mm-30) REVERT: J 143 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7267 (tm) REVERT: J 224 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8501 (mttp) outliers start: 40 outliers final: 12 residues processed: 183 average time/residue: 1.7514 time to fit residues: 349.0088 Evaluate side-chains 181 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 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 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 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 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: 2.9990 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 D 115 ASN E 115 ASN F 115 ASN G 115 ASN I 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.057984 restraints weight = 25418.237| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 1.93 r_work: 0.2602 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 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 : 0.004 0.021 17090 Z= 0.188 Angle : 0.449 5.051 23090 Z= 0.245 Chirality : 0.042 0.122 2720 Planarity : 0.002 0.020 2970 Dihedral : 4.211 15.460 2390 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.75 % Allowed : 16.78 % 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: 2.26 (0.19), residues: 2240 helix: 3.13 (0.19), residues: 760 sheet: 0.48 (0.17), residues: 840 loop : 1.09 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 113 HIS 0.001 0.000 HIS H 208 PHE 0.008 0.002 PHE C 225 TYR 0.007 0.001 TYR B 93 ARG 0.002 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 731) hydrogen bonds : angle 3.84597 ( 2073) covalent geometry : bond 0.00417 (17090) covalent geometry : angle 0.44857 (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 189 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.991 Fit side-chains REVERT: A 109 GLU cc_start: 0.8540 (tp30) cc_final: 0.8116 (tp30) REVERT: A 115 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7579 (p0) REVERT: A 143 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7307 (tm) REVERT: A 224 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8483 (mttp) REVERT: B 143 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7344 (tm) REVERT: B 224 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8427 (mttp) REVERT: C 109 GLU cc_start: 0.8477 (tp30) cc_final: 0.8246 (tp30) REVERT: C 143 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7426 (tm) REVERT: C 224 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8513 (mtpp) REVERT: D 109 GLU cc_start: 0.8571 (tp30) cc_final: 0.8317 (tp30) REVERT: D 143 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7183 (tm) REVERT: D 224 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8501 (mmtp) REVERT: E 143 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7333 (tm) REVERT: E 224 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8448 (mttp) REVERT: F 109 GLU cc_start: 0.8552 (tp30) cc_final: 0.8133 (tp30) REVERT: F 115 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7571 (p0) REVERT: F 143 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7286 (tm) REVERT: F 224 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8464 (mttp) REVERT: G 143 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7322 (tm) REVERT: G 224 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8433 (mttp) REVERT: H 109 GLU cc_start: 0.8481 (tp30) cc_final: 0.8243 (tp30) REVERT: H 143 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7425 (tm) REVERT: H 224 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8515 (mtpp) REVERT: I 109 GLU cc_start: 0.8573 (tp30) cc_final: 0.8276 (tp30) REVERT: I 143 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7363 (tm) REVERT: I 224 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8494 (mmtp) REVERT: J 109 GLU cc_start: 0.8478 (tp30) cc_final: 0.7884 (mm-30) REVERT: J 143 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7329 (tm) REVERT: J 224 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8457 (mttp) outliers start: 31 outliers final: 12 residues processed: 184 average time/residue: 1.7783 time to fit residues: 355.0903 Evaluate side-chains 182 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 164 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 115 ASN D 115 ASN E 115 ASN G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.090683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058352 restraints weight = 25578.188| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.94 r_work: 0.2611 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 17090 Z= 0.162 Angle : 0.429 5.025 23090 Z= 0.234 Chirality : 0.042 0.122 2720 Planarity : 0.002 0.032 2970 Dihedral : 4.084 14.967 2390 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.64 % Allowed : 16.84 % Favored : 81.53 % 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: 3.19 (0.19), residues: 760 sheet: 0.52 (0.17), residues: 840 loop : 1.06 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 113 HIS 0.001 0.000 HIS C 208 PHE 0.007 0.002 PHE C 225 TYR 0.007 0.001 TYR F 93 ARG 0.008 0.000 ARG G 190 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 731) hydrogen bonds : angle 3.79638 ( 2073) covalent geometry : bond 0.00357 (17090) covalent geometry : angle 0.42869 (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 187 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 2.084 Fit side-chains REVERT: A 109 GLU cc_start: 0.8571 (tp30) cc_final: 0.8175 (tp30) REVERT: A 143 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7326 (tm) REVERT: A 224 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8482 (mttp) REVERT: B 143 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7311 (tm) REVERT: B 224 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8403 (mttm) REVERT: C 109 GLU cc_start: 0.8484 (tp30) cc_final: 0.8236 (tp30) REVERT: C 143 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7411 (tm) REVERT: C 224 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8491 (mtpp) REVERT: D 109 GLU cc_start: 0.8588 (tp30) cc_final: 0.8334 (tp30) REVERT: D 143 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7140 (tm) REVERT: D 224 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8493 (mmtp) REVERT: E 109 GLU cc_start: 0.8324 (tp30) cc_final: 0.7905 (mm-30) REVERT: E 143 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7333 (tm) REVERT: E 224 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8430 (mttp) REVERT: F 109 GLU cc_start: 0.8578 (tp30) cc_final: 0.8197 (tp30) REVERT: F 143 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7345 (tm) REVERT: F 224 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8460 (mttp) REVERT: G 143 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7312 (tm) REVERT: G 224 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8403 (mttm) REVERT: H 109 GLU cc_start: 0.8459 (tp30) cc_final: 0.8237 (tp30) REVERT: H 143 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7398 (tm) REVERT: H 224 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8494 (mtpp) REVERT: I 109 GLU cc_start: 0.8592 (tp30) cc_final: 0.8331 (tp30) REVERT: I 143 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7298 (tm) REVERT: I 224 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8487 (mmtp) REVERT: J 109 GLU cc_start: 0.8488 (tp30) cc_final: 0.7886 (mm-30) REVERT: J 143 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7289 (tm) REVERT: J 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8442 (mttp) outliers start: 29 outliers final: 12 residues processed: 183 average time/residue: 1.7310 time to fit residues: 344.1777 Evaluate side-chains 180 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 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 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 143 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: 1.9990 chunk 105 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 D 115 ASN E 115 ASN F 115 ASN G 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.058227 restraints weight = 25779.674| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.96 r_work: 0.2612 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 17090 Z= 0.163 Angle : 0.425 4.985 23090 Z= 0.233 Chirality : 0.042 0.121 2720 Planarity : 0.002 0.034 2970 Dihedral : 4.050 14.890 2390 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.64 % Allowed : 16.78 % Favored : 81.58 % 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: 0.53 (0.18), residues: 840 loop : 1.06 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 113 HIS 0.001 0.000 HIS C 208 PHE 0.007 0.002 PHE C 225 TYR 0.007 0.001 TYR A 93 ARG 0.008 0.000 ARG G 190 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 731) hydrogen bonds : angle 3.77983 ( 2073) covalent geometry : bond 0.00360 (17090) covalent geometry : angle 0.42541 (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 188 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.871 Fit side-chains REVERT: A 109 GLU cc_start: 0.8539 (tp30) cc_final: 0.8145 (tp30) REVERT: A 143 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7340 (tm) REVERT: A 224 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8481 (mttp) REVERT: B 143 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7281 (tm) REVERT: B 224 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8401 (mttm) REVERT: C 109 GLU cc_start: 0.8487 (tp30) cc_final: 0.8235 (tp30) REVERT: C 143 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7407 (tm) REVERT: C 224 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8491 (mtpp) REVERT: D 109 GLU cc_start: 0.8608 (tp30) cc_final: 0.8160 (mm-30) REVERT: D 115 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7207 (p0) REVERT: D 143 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7134 (tm) REVERT: D 224 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8497 (mmtp) REVERT: E 109 GLU cc_start: 0.8334 (tp30) cc_final: 0.7864 (mm-30) REVERT: E 143 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7340 (tm) REVERT: E 224 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8430 (mttp) REVERT: E 238 LYS cc_start: 0.9102 (mtpm) cc_final: 0.8832 (tppp) REVERT: F 109 GLU cc_start: 0.8534 (tp30) cc_final: 0.8140 (tp30) REVERT: F 143 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7330 (tm) REVERT: F 224 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8453 (mttp) REVERT: G 143 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7289 (tm) REVERT: G 224 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8404 (mttm) REVERT: H 109 GLU cc_start: 0.8475 (tp30) cc_final: 0.8237 (tp30) REVERT: H 143 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7409 (tm) REVERT: H 224 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8494 (mtpp) REVERT: I 109 GLU cc_start: 0.8589 (tp30) cc_final: 0.8289 (tp30) REVERT: I 143 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7135 (tm) REVERT: I 224 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8489 (mmtp) REVERT: J 109 GLU cc_start: 0.8497 (tp30) cc_final: 0.7897 (mm-30) REVERT: J 143 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7321 (tm) REVERT: J 224 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8437 (mttp) outliers start: 29 outliers final: 14 residues processed: 183 average time/residue: 2.0719 time to fit residues: 411.5656 Evaluate side-chains 184 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 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 115 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 36 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 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: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.090726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058316 restraints weight = 25719.143| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.95 r_work: 0.2612 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 17090 Z= 0.167 Angle : 0.428 4.993 23090 Z= 0.234 Chirality : 0.042 0.121 2720 Planarity : 0.002 0.035 2970 Dihedral : 4.050 14.902 2390 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.69 % Allowed : 16.78 % Favored : 81.53 % 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: 2.35 (0.19), residues: 2240 helix: 3.22 (0.19), residues: 760 sheet: 0.54 (0.18), residues: 840 loop : 1.08 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 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 A 93 ARG 0.008 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 731) hydrogen bonds : angle 3.77262 ( 2073) covalent geometry : bond 0.00370 (17090) covalent geometry : angle 0.42781 (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 189 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 2.591 Fit side-chains REVERT: A 109 GLU cc_start: 0.8536 (tp30) cc_final: 0.8132 (tp30) REVERT: A 115 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7474 (p0) REVERT: A 143 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7364 (tm) REVERT: A 224 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8480 (mttp) REVERT: B 143 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7288 (tm) REVERT: B 224 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8405 (mttm) REVERT: C 109 GLU cc_start: 0.8469 (tp30) cc_final: 0.8216 (tp30) REVERT: C 143 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7399 (tm) REVERT: C 224 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8502 (mtpp) REVERT: D 109 GLU cc_start: 0.8609 (tp30) cc_final: 0.8181 (mm-30) REVERT: D 115 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7282 (p0) REVERT: D 143 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7159 (tm) REVERT: D 224 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8499 (mmtp) REVERT: E 109 GLU cc_start: 0.8350 (tp30) cc_final: 0.7890 (mm-30) REVERT: E 143 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7385 (tm) REVERT: E 224 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8431 (mttp) REVERT: E 238 LYS cc_start: 0.9107 (mtpm) cc_final: 0.8839 (tppp) REVERT: F 109 GLU cc_start: 0.8542 (tp30) cc_final: 0.8141 (tp30) REVERT: F 115 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7493 (p0) REVERT: F 143 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7342 (tm) REVERT: F 224 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8457 (mttp) REVERT: G 143 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7285 (tm) REVERT: G 224 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8407 (mttm) REVERT: H 109 GLU cc_start: 0.8480 (tp30) cc_final: 0.8251 (tp30) REVERT: H 143 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7401 (tm) REVERT: H 224 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8506 (mtpp) REVERT: I 109 GLU cc_start: 0.8556 (tp30) cc_final: 0.8244 (tp30) REVERT: I 143 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7156 (tm) REVERT: I 224 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8492 (mmtp) REVERT: J 109 GLU cc_start: 0.8491 (tp30) cc_final: 0.7887 (mm-30) REVERT: J 143 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7345 (tm) REVERT: J 224 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8442 (mttp) outliers start: 30 outliers final: 13 residues processed: 183 average time/residue: 2.2954 time to fit residues: 457.2385 Evaluate side-chains 185 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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 E residue 147 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 115 ASN 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=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: 0.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN D 115 ASN E 115 ASN G 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.090929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.058531 restraints weight = 25593.225| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.95 r_work: 0.2614 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 17090 Z= 0.147 Angle : 0.417 4.966 23090 Z= 0.228 Chirality : 0.041 0.120 2720 Planarity : 0.002 0.035 2970 Dihedral : 3.988 14.796 2390 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.58 % Allowed : 16.89 % Favored : 81.53 % 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: 2.37 (0.19), residues: 2240 helix: 3.24 (0.19), residues: 760 sheet: 0.56 (0.18), residues: 840 loop : 1.08 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 113 HIS 0.001 0.000 HIS C 208 PHE 0.006 0.002 PHE C 225 TYR 0.006 0.001 TYR F 93 ARG 0.008 0.000 ARG G 190 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 731) hydrogen bonds : angle 3.75796 ( 2073) covalent geometry : bond 0.00322 (17090) covalent geometry : angle 0.41691 (23090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19611.62 seconds wall clock time: 341 minutes 37.01 seconds (20497.01 seconds total)