Starting phenix.real_space_refine on Sun Aug 24 03:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2v_47469/08_2025/9e2v_47469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2v_47469/08_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_47469/08_2025/9e2v_47469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2v_47469/08_2025/9e2v_47469.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2v_47469/08_2025/9e2v_47469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2v_47469/08_2025/9e2v_47469.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.25, per 1000 atoms: 0.13 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: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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: 0.49 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: 2.68 Time building geometry restraints manager: 2.25 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 16.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG E 108 TYR 0.006 0.001 TYR B 93 PHE 0.006 0.001 PHE D 225 TRP 0.003 0.001 TRP D 45 HIS 0.001 0.000 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00239 (17090) covalent geometry : angle 0.40199 (23090) hydrogen bonds : bond 0.19885 ( 731) hydrogen bonds : angle 6.27207 ( 2073) *********************** 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 : 0.648 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: 0.9012 time to fit residues: 170.7988 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 : 0.668 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.090843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.058006 restraints weight = 25631.705| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.95 r_work: 0.2604 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 17090 Z= 0.252 Angle : 0.515 5.805 23090 Z= 0.279 Chirality : 0.044 0.127 2720 Planarity : 0.003 0.031 2970 Dihedral : 4.180 15.023 2399 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.39 % Allowed : 20.23 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.18), residues: 2240 helix: 1.85 (0.18), residues: 830 sheet: 1.03 (0.18), residues: 790 loop : 0.90 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 108 TYR 0.008 0.001 TYR B 210 PHE 0.011 0.003 PHE C 225 TRP 0.007 0.001 TRP D 94 HIS 0.001 0.000 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00571 (17090) covalent geometry : angle 0.51481 (23090) hydrogen bonds : bond 0.03807 ( 731) hydrogen bonds : angle 4.23711 ( 2073) *********************** 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 212 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.578 Fit side-chains REVERT: A 109 GLU cc_start: 0.8413 (tp30) cc_final: 0.8077 (tp30) REVERT: A 115 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7220 (p0) REVERT: A 143 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7263 (tm) REVERT: A 224 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8531 (mttp) REVERT: B 109 GLU cc_start: 0.8394 (tp30) cc_final: 0.8123 (tp30) REVERT: B 115 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 143 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7335 (tm) REVERT: B 224 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8417 (mttm) REVERT: C 109 GLU cc_start: 0.8363 (tp30) cc_final: 0.7926 (tp30) REVERT: C 115 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7230 (p0) REVERT: C 143 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7437 (tm) REVERT: C 224 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8456 (mmtp) REVERT: D 143 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7454 (tm) REVERT: D 224 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8462 (mmtp) REVERT: E 109 GLU cc_start: 0.8443 (tp30) cc_final: 0.8100 (tp30) REVERT: E 115 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7423 (p0) REVERT: E 143 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7432 (tm) REVERT: E 224 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8479 (mtpp) REVERT: F 109 GLU cc_start: 0.8444 (tp30) cc_final: 0.8112 (tp30) REVERT: F 115 ASN cc_start: 0.7460 (OUTLIER) cc_final: 0.7247 (p0) REVERT: F 143 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7266 (tm) REVERT: F 224 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8489 (mttp) REVERT: G 109 GLU cc_start: 0.8416 (tp30) cc_final: 0.8074 (tp30) REVERT: G 115 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7301 (p0) REVERT: G 143 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7305 (tm) REVERT: G 224 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8427 (mttm) REVERT: H 109 GLU cc_start: 0.8394 (tp30) cc_final: 0.8000 (tp30) REVERT: H 115 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7210 (p0) REVERT: H 143 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7425 (tm) REVERT: H 224 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8472 (mmtp) REVERT: I 143 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7449 (tm) REVERT: I 224 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8456 (mmtp) REVERT: J 143 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7194 (tm) REVERT: J 224 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8516 (mttp) outliers start: 60 outliers final: 10 residues processed: 202 average time/residue: 0.9527 time to fit residues: 206.8179 Evaluate side-chains 175 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 113 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.089994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.057121 restraints weight = 25820.031| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.95 r_work: 0.2582 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.1361 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= 0.297 Angle : 0.528 6.100 23090 Z= 0.284 Chirality : 0.045 0.126 2720 Planarity : 0.003 0.030 2970 Dihedral : 4.342 15.491 2390 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.98 % Allowed : 18.14 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.18), residues: 2240 helix: 2.10 (0.18), residues: 830 sheet: 0.83 (0.18), residues: 790 loop : 0.72 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 108 TYR 0.008 0.001 TYR B 210 PHE 0.011 0.003 PHE H 225 TRP 0.006 0.001 TRP D 94 HIS 0.001 0.000 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00675 (17090) covalent geometry : angle 0.52805 (23090) hydrogen bonds : bond 0.03838 ( 731) hydrogen bonds : angle 4.09912 ( 2073) *********************** 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 188 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.662 Fit side-chains REVERT: A 109 GLU cc_start: 0.8515 (tp30) cc_final: 0.8195 (tp30) REVERT: A 115 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7380 (p0) REVERT: A 143 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7207 (tm) REVERT: A 224 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8529 (mttp) REVERT: B 115 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 143 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7362 (tm) REVERT: B 224 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8412 (mttp) REVERT: C 143 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7425 (tm) REVERT: C 224 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8502 (mttp) REVERT: D 143 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7237 (tm) REVERT: D 224 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8476 (mmtp) REVERT: E 143 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7384 (tm) REVERT: E 224 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8479 (mttp) REVERT: F 109 GLU cc_start: 0.8531 (tp30) cc_final: 0.8215 (tp30) REVERT: F 115 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (p0) REVERT: F 143 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7246 (tm) REVERT: F 224 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8497 (mttp) REVERT: G 143 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7325 (tm) REVERT: G 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8414 (mttp) REVERT: H 143 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7456 (tm) REVERT: H 224 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8528 (mtpp) REVERT: I 143 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7216 (tm) REVERT: I 224 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8466 (mmtp) REVERT: J 224 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8480 (mttp) outliers start: 35 outliers final: 9 residues processed: 177 average time/residue: 0.8721 time to fit residues: 167.0033 Evaluate side-chains 173 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 56 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 170 optimal weight: 0.0970 chunk 200 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.090668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.058201 restraints weight = 25768.399| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.95 r_work: 0.2610 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 17090 Z= 0.177 Angle : 0.445 5.462 23090 Z= 0.241 Chirality : 0.042 0.122 2720 Planarity : 0.002 0.017 2970 Dihedral : 4.099 14.917 2390 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.15 % Allowed : 17.57 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.18), residues: 2240 helix: 2.37 (0.18), residues: 830 sheet: 0.71 (0.18), residues: 820 loop : 0.67 (0.28), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 190 TYR 0.006 0.001 TYR F 93 PHE 0.007 0.002 PHE H 225 TRP 0.003 0.001 TRP I 94 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00391 (17090) covalent geometry : angle 0.44519 (23090) hydrogen bonds : bond 0.03178 ( 731) hydrogen bonds : angle 3.90811 ( 2073) *********************** 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 194 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.709 Fit side-chains REVERT: A 109 GLU cc_start: 0.8540 (tp30) cc_final: 0.8112 (tp30) REVERT: A 115 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7380 (p0) REVERT: A 143 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7277 (tm) REVERT: A 224 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8492 (mttp) REVERT: B 143 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7346 (tm) REVERT: B 224 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8419 (mttm) REVERT: C 109 GLU cc_start: 0.8355 (tp30) cc_final: 0.8054 (tp30) REVERT: C 143 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7420 (tm) REVERT: C 224 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8491 (mttp) REVERT: D 109 GLU cc_start: 0.8512 (tp30) cc_final: 0.8202 (tp30) REVERT: D 115 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7274 (p0) REVERT: D 143 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7288 (tm) REVERT: D 224 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8483 (mmtp) REVERT: E 109 GLU cc_start: 0.8427 (tp30) cc_final: 0.8170 (tp30) REVERT: E 143 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7371 (tm) REVERT: E 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8437 (mttp) REVERT: F 109 GLU cc_start: 0.8545 (tp30) cc_final: 0.8119 (tp30) REVERT: F 115 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7374 (p0) REVERT: F 143 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7314 (tm) REVERT: F 224 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8463 (mttp) REVERT: G 115 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7215 (p0) REVERT: G 143 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7304 (tm) REVERT: G 224 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8427 (mttm) REVERT: H 109 GLU cc_start: 0.8313 (tp30) cc_final: 0.8065 (tp30) REVERT: H 143 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7471 (tm) REVERT: H 224 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8508 (mtpp) REVERT: I 109 GLU cc_start: 0.8410 (tp30) cc_final: 0.8113 (tp30) REVERT: I 143 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7293 (tm) REVERT: I 224 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8489 (mmtp) REVERT: J 109 GLU cc_start: 0.8462 (tp30) cc_final: 0.7912 (mm-30) REVERT: J 143 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7179 (tm) REVERT: J 224 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8458 (mttp) outliers start: 38 outliers final: 15 residues processed: 188 average time/residue: 0.8018 time to fit residues: 163.7255 Evaluate side-chains 185 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 115 ASN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 183 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.090330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.057945 restraints weight = 25679.496| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.95 r_work: 0.2608 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 17090 Z= 0.221 Angle : 0.465 5.437 23090 Z= 0.253 Chirality : 0.043 0.123 2720 Planarity : 0.002 0.024 2970 Dihedral : 4.193 15.282 2390 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.75 % Allowed : 17.91 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.19), residues: 2240 helix: 3.10 (0.18), residues: 760 sheet: 0.65 (0.18), residues: 840 loop : 1.09 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 190 TYR 0.006 0.001 TYR A 93 PHE 0.009 0.002 PHE C 225 TRP 0.005 0.001 TRP C 113 HIS 0.001 0.000 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00496 (17090) covalent geometry : angle 0.46530 (23090) hydrogen bonds : bond 0.03301 ( 731) hydrogen bonds : angle 3.89305 ( 2073) *********************** 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 189 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.537 Fit side-chains REVERT: A 109 GLU cc_start: 0.8589 (tp30) cc_final: 0.8178 (tp30) REVERT: A 115 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7577 (p0) REVERT: A 143 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7274 (tm) REVERT: A 224 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8485 (mttp) REVERT: B 109 GLU cc_start: 0.8391 (tp30) cc_final: 0.8147 (tp30) REVERT: B 143 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7395 (tm) REVERT: B 224 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8436 (mttm) REVERT: C 109 GLU cc_start: 0.8483 (tp30) cc_final: 0.8191 (tp30) REVERT: C 143 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7390 (tm) REVERT: C 224 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8517 (mtpp) REVERT: D 109 GLU cc_start: 0.8618 (tp30) cc_final: 0.8311 (tp30) REVERT: D 115 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7479 (p0) REVERT: D 143 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7224 (tm) REVERT: D 224 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8507 (mmtp) REVERT: E 109 GLU cc_start: 0.8511 (tp30) cc_final: 0.8187 (tp30) REVERT: E 115 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7425 (p0) REVERT: E 143 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7345 (tm) REVERT: E 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8451 (mttp) REVERT: F 109 GLU cc_start: 0.8595 (tp30) cc_final: 0.8183 (tp30) REVERT: F 115 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7581 (p0) REVERT: F 143 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7324 (tm) REVERT: F 224 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8480 (mttp) REVERT: G 143 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7325 (tm) REVERT: G 224 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8430 (mttm) REVERT: H 109 GLU cc_start: 0.8470 (tp30) cc_final: 0.8233 (tp30) REVERT: H 143 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7436 (tm) REVERT: H 224 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8521 (mtpp) REVERT: I 109 GLU cc_start: 0.8570 (tp30) cc_final: 0.8326 (tp30) REVERT: I 143 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7239 (tm) REVERT: I 224 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8495 (mmtp) REVERT: J 109 GLU cc_start: 0.8478 (tp30) cc_final: 0.7941 (mm-30) REVERT: J 143 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7137 (tm) REVERT: J 224 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8466 (mttp) outliers start: 31 outliers final: 13 residues processed: 183 average time/residue: 0.8438 time to fit residues: 167.0110 Evaluate side-chains 185 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 143 LEU Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 153 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 G 115 ASN H 115 ASN I 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.058557 restraints weight = 25607.273| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.95 r_work: 0.2618 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 17090 Z= 0.144 Angle : 0.414 4.969 23090 Z= 0.227 Chirality : 0.041 0.119 2720 Planarity : 0.002 0.015 2970 Dihedral : 3.965 14.686 2390 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.53 % Allowed : 17.46 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.19), residues: 2240 helix: 3.24 (0.18), residues: 760 sheet: 0.67 (0.18), residues: 840 loop : 1.07 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 190 TYR 0.006 0.001 TYR J 93 PHE 0.006 0.002 PHE C 225 TRP 0.005 0.001 TRP C 113 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00312 (17090) covalent geometry : angle 0.41377 (23090) hydrogen bonds : bond 0.02910 ( 731) hydrogen bonds : angle 3.76766 ( 2073) *********************** 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 187 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.791 Fit side-chains REVERT: A 109 GLU cc_start: 0.8595 (tp30) cc_final: 0.8234 (tp30) REVERT: A 143 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7314 (tm) REVERT: A 224 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8463 (mttp) REVERT: B 143 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7408 (tm) REVERT: B 224 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8407 (mttm) REVERT: C 143 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7441 (tm) REVERT: C 224 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8486 (mtpp) REVERT: D 109 GLU cc_start: 0.8590 (tp30) cc_final: 0.8119 (mm-30) REVERT: D 143 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7267 (tm) REVERT: D 224 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8474 (mmtp) REVERT: E 109 GLU cc_start: 0.8515 (tp30) cc_final: 0.7993 (mm-30) REVERT: E 143 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7395 (tm) REVERT: E 224 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8441 (mttp) REVERT: E 238 LYS cc_start: 0.9079 (mtpm) cc_final: 0.8814 (tppp) REVERT: F 109 GLU cc_start: 0.8607 (tp30) cc_final: 0.8248 (tp30) REVERT: F 143 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7319 (tm) REVERT: F 224 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8447 (mttp) REVERT: G 143 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7390 (tm) REVERT: G 224 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8415 (mttm) REVERT: H 109 GLU cc_start: 0.8438 (tp30) cc_final: 0.8170 (tp30) REVERT: H 143 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7491 (tm) REVERT: H 224 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8485 (mtpp) REVERT: I 109 GLU cc_start: 0.8561 (tp30) cc_final: 0.8289 (tp30) REVERT: I 143 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7236 (tm) REVERT: I 224 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8475 (mmtp) REVERT: J 109 GLU cc_start: 0.8471 (tp30) cc_final: 0.7850 (mm-30) REVERT: J 143 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7177 (tm) REVERT: J 224 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8443 (mttp) outliers start: 27 outliers final: 12 residues processed: 181 average time/residue: 0.9036 time to fit residues: 176.5046 Evaluate side-chains 182 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU 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 I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 52 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 115 ASN D 115 ASN E 115 ASN F 115 ASN G 115 ASN I 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.057899 restraints weight = 25493.387| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.94 r_work: 0.2601 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 17090 Z= 0.210 Angle : 0.452 5.291 23090 Z= 0.246 Chirality : 0.043 0.122 2720 Planarity : 0.002 0.022 2970 Dihedral : 4.128 15.060 2390 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.86 % Allowed : 16.78 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.19), residues: 2240 helix: 3.21 (0.18), residues: 760 sheet: 0.62 (0.18), residues: 840 loop : 1.08 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.006 0.001 TYR F 93 PHE 0.009 0.002 PHE C 225 TRP 0.004 0.001 TRP I 94 HIS 0.001 0.000 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00470 (17090) covalent geometry : angle 0.45202 (23090) hydrogen bonds : bond 0.03144 ( 731) hydrogen bonds : angle 3.82010 ( 2073) *********************** 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 193 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.735 Fit side-chains REVERT: A 109 GLU cc_start: 0.8581 (tp30) cc_final: 0.8188 (tp30) REVERT: A 115 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7425 (p0) REVERT: A 143 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7311 (tm) REVERT: A 224 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8474 (mttp) REVERT: B 143 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7399 (tm) REVERT: B 224 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8406 (mttm) REVERT: C 109 GLU cc_start: 0.8454 (tp30) cc_final: 0.8241 (tp30) REVERT: C 143 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7419 (tm) REVERT: C 224 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8496 (mtpp) REVERT: D 109 GLU cc_start: 0.8567 (tp30) cc_final: 0.8251 (tp30) REVERT: D 115 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7494 (p0) REVERT: D 143 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7214 (tm) REVERT: D 224 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8492 (mmtp) REVERT: E 109 GLU cc_start: 0.8495 (tp30) cc_final: 0.8203 (tp30) REVERT: E 143 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7347 (tm) REVERT: E 224 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8443 (mttp) REVERT: F 109 GLU cc_start: 0.8591 (tp30) cc_final: 0.8200 (tp30) REVERT: F 115 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7432 (p0) REVERT: F 143 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7324 (tm) REVERT: F 224 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8466 (mttp) REVERT: G 143 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7396 (tm) REVERT: G 224 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8409 (mttm) REVERT: H 143 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7438 (tm) REVERT: H 224 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8493 (mtpp) REVERT: I 109 GLU cc_start: 0.8594 (tp30) cc_final: 0.8320 (tp30) REVERT: I 143 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7222 (tm) REVERT: I 224 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8491 (mmtp) REVERT: J 109 GLU cc_start: 0.8476 (tp30) cc_final: 0.7876 (mm-30) REVERT: J 143 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7217 (tm) REVERT: J 224 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8453 (mttp) outliers start: 33 outliers final: 15 residues processed: 186 average time/residue: 0.9248 time to fit residues: 185.7242 Evaluate side-chains 188 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 115 ASN Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN G 115 ASN H 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.057772 restraints weight = 25680.418| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.95 r_work: 0.2597 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 17090 Z= 0.219 Angle : 0.459 5.383 23090 Z= 0.249 Chirality : 0.043 0.123 2720 Planarity : 0.002 0.023 2970 Dihedral : 4.165 15.194 2390 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.69 % Allowed : 16.89 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.19), residues: 2240 helix: 3.20 (0.18), residues: 760 sheet: 0.60 (0.18), residues: 840 loop : 1.11 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.006 0.001 TYR A 93 PHE 0.009 0.002 PHE H 225 TRP 0.004 0.001 TRP I 94 HIS 0.001 0.000 HIS H 208 Details of bonding type rmsd covalent geometry : bond 0.00491 (17090) covalent geometry : angle 0.45894 (23090) hydrogen bonds : bond 0.03168 ( 731) hydrogen bonds : angle 3.82889 ( 2073) *********************** 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 190 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.730 Fit side-chains REVERT: A 109 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: A 143 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7318 (tm) REVERT: A 224 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8481 (mttp) REVERT: B 143 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7313 (tm) REVERT: B 224 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8383 (mttm) REVERT: C 109 GLU cc_start: 0.8458 (tp30) cc_final: 0.8252 (tp30) REVERT: C 143 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7376 (tm) REVERT: C 224 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8500 (mtpp) REVERT: D 109 GLU cc_start: 0.8592 (tp30) cc_final: 0.8300 (tp30) REVERT: D 143 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7209 (tm) REVERT: D 224 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8479 (mmtp) REVERT: E 109 GLU cc_start: 0.8528 (tp30) cc_final: 0.8234 (tp30) REVERT: E 143 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7361 (tm) REVERT: E 224 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8434 (mttp) REVERT: F 109 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: F 143 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7284 (tm) REVERT: F 224 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8478 (mttp) REVERT: G 143 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7367 (tm) REVERT: G 224 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8381 (mttm) REVERT: H 143 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7354 (tm) REVERT: H 224 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8503 (mtpp) REVERT: I 109 GLU cc_start: 0.8600 (tp30) cc_final: 0.8328 (tp30) REVERT: I 143 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7224 (tm) REVERT: I 224 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8462 (mmtp) REVERT: J 109 GLU cc_start: 0.8498 (tp30) cc_final: 0.7906 (mm-30) REVERT: J 143 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7187 (tm) REVERT: J 224 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8443 (mttp) outliers start: 30 outliers final: 13 residues processed: 180 average time/residue: 0.9708 time to fit residues: 188.3943 Evaluate side-chains 185 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 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 I residue 147 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8472 > 50: distance: 56 - 62: 5.261 distance: 62 - 63: 10.747 distance: 63 - 64: 15.328 distance: 63 - 66: 20.422 distance: 64 - 65: 5.966 distance: 64 - 69: 8.281 distance: 66 - 67: 6.375 distance: 66 - 68: 7.740 distance: 69 - 70: 8.921 distance: 70 - 71: 16.632 distance: 70 - 73: 11.464 distance: 71 - 72: 11.343 distance: 71 - 75: 24.391 distance: 75 - 76: 14.166 distance: 76 - 77: 19.499 distance: 76 - 79: 15.477 distance: 77 - 78: 16.163 distance: 77 - 83: 18.403 distance: 79 - 80: 7.341 distance: 80 - 81: 4.689 distance: 80 - 82: 13.032 distance: 83 - 84: 10.738 distance: 84 - 85: 22.274 distance: 84 - 87: 16.077 distance: 85 - 86: 22.882 distance: 85 - 92: 16.142 distance: 87 - 88: 6.076 distance: 88 - 89: 10.666 distance: 89 - 90: 10.726 distance: 90 - 91: 6.630 distance: 92 - 93: 15.927 distance: 93 - 94: 22.834 distance: 93 - 96: 10.487 distance: 94 - 95: 12.239 distance: 94 - 100: 15.973 distance: 96 - 97: 6.067 distance: 97 - 98: 5.286 distance: 97 - 99: 12.374 distance: 100 - 101: 8.013 distance: 101 - 102: 12.011 distance: 101 - 104: 4.188 distance: 102 - 103: 9.574 distance: 102 - 108: 7.608 distance: 104 - 105: 8.113 distance: 105 - 106: 7.467 distance: 106 - 107: 9.642 distance: 108 - 109: 7.600 distance: 109 - 110: 34.735 distance: 109 - 112: 10.685 distance: 110 - 111: 18.270 distance: 110 - 114: 49.284 distance: 112 - 113: 6.839 distance: 114 - 115: 50.847 distance: 115 - 116: 21.898 distance: 116 - 117: 10.253 distance: 116 - 118: 14.752 distance: 117 - 139: 10.114 distance: 118 - 119: 8.037 distance: 119 - 120: 6.961 distance: 119 - 122: 4.092 distance: 120 - 121: 10.798 distance: 120 - 126: 8.192 distance: 122 - 123: 8.109 distance: 123 - 124: 6.773 distance: 123 - 125: 6.514 distance: 126 - 127: 7.972 distance: 127 - 128: 10.214 distance: 127 - 130: 5.346 distance: 128 - 129: 7.629 distance: 128 - 135: 9.376 distance: 129 - 155: 4.416 distance: 130 - 131: 3.055