Starting phenix.real_space_refine on Thu Mar 5 08:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v00_26924/03_2026/7v00_26924_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v00_26924/03_2026/7v00_26924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v00_26924/03_2026/7v00_26924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v00_26924/03_2026/7v00_26924.map" model { file = "/net/cci-nas-00/data/ceres_data/7v00_26924/03_2026/7v00_26924_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v00_26924/03_2026/7v00_26924_neut.cif" } resolution = 3.87 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= 0.030 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 56 5.16 5 C 12877 2.51 5 N 3440 2.21 5 O 4011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20420 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2473 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 3 Chain: "F" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5652 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 7, 'TRANS': 687} Chain breaks: 3 Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 637 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.16, per 1000 atoms: 0.20 Number of scatterers: 20420 At special positions: 0 Unit cell: (93.003, 120.797, 209.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 36 15.00 O 4011 8.00 N 3440 7.00 C 12877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 892.1 milliseconds 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 28 sheets defined 48.4% alpha, 15.7% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.696A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.771A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.685A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 62 removed outlier: 3.501A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.564A pdb=" N ASN B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.559A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 4.446A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.764A pdb=" N GLY C 188 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.625A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.587A pdb=" N ASN D 114 " --> pdb=" O HIS D 110 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.687A pdb=" N GLN E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 removed outlier: 3.678A pdb=" N ILE E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 removed outlier: 4.191A pdb=" N SER E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 230 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 278 through 293 Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.709A pdb=" N MET E 300 " --> pdb=" O TYR E 297 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 303 " --> pdb=" O MET E 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 16 through 24 removed outlier: 3.872A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.653A pdb=" N LEU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 67 removed outlier: 4.096A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 116 through 122 removed outlier: 4.490A pdb=" N ILE F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.246A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.900A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 removed outlier: 3.596A pdb=" N SER F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.612A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.774A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 437 removed outlier: 4.530A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.885A pdb=" N ASN F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 550 through 573 removed outlier: 3.625A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 612 Processing helix chain 'F' and resid 630 through 636 removed outlier: 3.990A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 removed outlier: 4.005A pdb=" N ASN F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 734 Processing helix chain 'F' and resid 735 through 750 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.907A pdb=" N GLU I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 47 Processing helix chain 'J' and resid 48 through 61 Processing helix chain 'J' and resid 75 through 92 removed outlier: 3.646A pdb=" N GLU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 removed outlier: 5.083A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.889A pdb=" N TYR K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 5.574A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 9 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS A 4 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A 201 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 6 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 199 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 8 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 197 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.511A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.471A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.649A pdb=" N LEU D 96 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN D 155 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE D 98 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE D 153 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP D 100 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL D 151 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.510A pdb=" N LEU D 43 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 119 through 124 Processing sheet with id=AB3, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.938A pdb=" N GLN E 22 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 41 Processing sheet with id=AB6, first strand: chain 'E' and resid 184 through 193 removed outlier: 7.185A pdb=" N MET E 186 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP E 178 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 188 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.569A pdb=" N TYR F 316 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR F 310 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AB9, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.678A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 461 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 578 through 584 removed outlier: 7.402A pdb=" N ILE F 578 " --> pdb=" O ALA F 593 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA F 593 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.518A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC5, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC6, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AC7, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.693A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC9, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.552A pdb=" N LYS I 26 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 38 " --> pdb=" O LYS I 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'J' and resid 25 through 26 939 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6038 1.33 - 1.46: 4261 1.46 - 1.58: 10386 1.58 - 1.70: 70 1.70 - 1.82: 99 Bond restraints: 20854 Sorted by residual: bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.475 1.386 0.089 1.50e-02 4.44e+03 3.50e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.480 1.567 -0.087 1.50e-02 4.44e+03 3.33e+01 bond pdb=" C1' C G 28 " pdb=" N1 C G 28 " ideal model delta sigma weight residual 1.480 1.565 -0.085 1.50e-02 4.44e+03 3.19e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.475 1.402 0.073 1.50e-02 4.44e+03 2.38e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.470 1.540 -0.070 1.50e-02 4.44e+03 2.16e+01 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27271 2.13 - 4.27: 758 4.27 - 6.40: 128 6.40 - 8.53: 20 8.53 - 10.66: 4 Bond angle restraints: 28181 Sorted by residual: angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 130.39 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 107.01 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" C THR F 539 " pdb=" N PHE F 540 " pdb=" CA PHE F 540 " ideal model delta sigma weight residual 120.31 111.85 8.46 1.52e+00 4.33e-01 3.10e+01 angle pdb=" C5' ATP F 801 " pdb=" O5' ATP F 801 " pdb=" PA ATP F 801 " ideal model delta sigma weight residual 121.27 116.99 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N MET E 186 " pdb=" CA MET E 186 " pdb=" C MET E 186 " ideal model delta sigma weight residual 110.07 104.81 5.26 1.26e+00 6.30e-01 1.74e+01 ... (remaining 28176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 12230 31.68 - 63.35: 327 63.35 - 95.03: 42 95.03 - 126.70: 4 126.70 - 158.37: 3 Dihedral angle restraints: 12606 sinusoidal: 5528 harmonic: 7078 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 50.60 149.40 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -158.23 72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 30.37 -158.37 1 1.70e+01 3.46e-03 6.41e+01 ... (remaining 12603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2509 0.066 - 0.132: 516 0.132 - 0.198: 53 0.198 - 0.264: 8 0.264 - 0.330: 3 Chirality restraints: 3089 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE D 46 " pdb=" CA ILE D 46 " pdb=" CG1 ILE D 46 " pdb=" CG2 ILE D 46 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3086 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.08e-02 2.38e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 339 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 129 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C THR F 129 " 0.067 2.00e-02 2.50e+03 pdb=" O THR F 129 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN F 130 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 85 " -0.022 2.00e-02 2.50e+03 2.20e-02 8.49e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.001 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 17450 3.15 - 3.73: 30144 3.73 - 4.32: 42625 4.32 - 4.90: 69362 Nonbonded interactions: 159737 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.987 3.120 nonbonded pdb=" O TYR H 71 " pdb=" OH TYR H 162 " model vdw 2.035 3.040 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.056 3.040 nonbonded pdb=" NH1 ARG C 129 " pdb=" OD1 ASN D 57 " model vdw 2.057 3.120 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.118 3.040 ... (remaining 159732 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'B' and resid 2 through 208) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 139)) selection = chain 'J' selection = (chain 'K' and (resid 17 through 61 or resid 74 through 139)) } 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 group one per residue 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.350 Find NCS groups from input model: 0.150 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.006 0.092 20855 Z= 0.323 Angle : 0.862 10.663 28183 Z= 0.497 Chirality : 0.053 0.330 3089 Planarity : 0.004 0.065 3493 Dihedral : 14.507 158.375 8053 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 0.32 % Allowed : 0.69 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.16), residues: 2378 helix: 0.09 (0.15), residues: 1038 sheet: 0.13 (0.26), residues: 387 loop : -1.82 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 137 TYR 0.030 0.002 TYR F 582 PHE 0.051 0.003 PHE I 85 TRP 0.079 0.004 TRP F 339 HIS 0.007 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00589 (20854) covalent geometry : angle 0.86219 (28181) SS BOND : bond 0.00118 ( 1) SS BOND : angle 1.35683 ( 2) hydrogen bonds : bond 0.18188 ( 935) hydrogen bonds : angle 7.14156 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 444 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 110 HIS cc_start: 0.8270 (t-90) cc_final: 0.7697 (t-170) REVERT: D 131 THR cc_start: 0.8024 (p) cc_final: 0.7390 (p) REVERT: E 28 ASP cc_start: 0.8385 (m-30) cc_final: 0.7786 (m-30) REVERT: E 33 PHE cc_start: 0.8218 (m-10) cc_final: 0.7706 (m-80) REVERT: E 41 ILE cc_start: 0.8233 (mm) cc_final: 0.8017 (mp) REVERT: F 222 ASP cc_start: 0.8014 (m-30) cc_final: 0.7805 (m-30) REVERT: F 624 MET cc_start: 0.7867 (ttm) cc_final: 0.7514 (tpt) REVERT: I 85 PHE cc_start: 0.8837 (m-80) cc_final: 0.8540 (m-80) REVERT: I 104 MET cc_start: 0.8553 (mmm) cc_final: 0.8349 (tmm) REVERT: I 119 PHE cc_start: 0.9040 (t80) cc_final: 0.8747 (t80) REVERT: J 18 HIS cc_start: 0.7377 (t-170) cc_final: 0.6669 (t70) REVERT: J 126 TYR cc_start: 0.8998 (t80) cc_final: 0.8745 (t80) REVERT: K 50 ASN cc_start: 0.8962 (m-40) cc_final: 0.8045 (m110) outliers start: 7 outliers final: 0 residues processed: 449 average time/residue: 0.1779 time to fit residues: 114.9459 Evaluate side-chains 230 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 168 ASN D 174 HIS D 178 ASN E 60 GLN E 316 ASN E 324 GLN F 14 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 482 ASN F 560 GLN F 670 ASN F 708 ASN H 214 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.061515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.047168 restraints weight = 140704.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.048545 restraints weight = 82056.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.049420 restraints weight = 55972.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050004 restraints weight = 42876.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050388 restraints weight = 35704.600| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20855 Z= 0.161 Angle : 0.729 10.885 28183 Z= 0.387 Chirality : 0.046 0.257 3089 Planarity : 0.004 0.042 3493 Dihedral : 13.830 161.744 3140 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.11 % Allowed : 9.96 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2378 helix: 0.52 (0.16), residues: 1074 sheet: 0.39 (0.26), residues: 390 loop : -1.56 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 64 TYR 0.029 0.002 TYR J 86 PHE 0.036 0.002 PHE K 85 TRP 0.035 0.002 TRP F 339 HIS 0.010 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00340 (20854) covalent geometry : angle 0.72929 (28181) SS BOND : bond 0.00222 ( 1) SS BOND : angle 1.11952 ( 2) hydrogen bonds : bond 0.04992 ( 935) hydrogen bonds : angle 5.40499 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8983 (tmm) cc_final: 0.8775 (tmm) REVERT: D 67 MET cc_start: 0.8391 (tmm) cc_final: 0.8061 (tmm) REVERT: E 28 ASP cc_start: 0.8759 (m-30) cc_final: 0.8411 (t0) REVERT: E 66 PRO cc_start: 0.8557 (Cg_exo) cc_final: 0.8264 (Cg_endo) REVERT: E 186 MET cc_start: 0.8707 (mmm) cc_final: 0.8043 (mpp) REVERT: E 259 PHE cc_start: 0.7877 (m-10) cc_final: 0.7423 (m-10) REVERT: E 327 MET cc_start: 0.9287 (ptm) cc_final: 0.9073 (ptp) REVERT: F 184 TRP cc_start: 0.5591 (m100) cc_final: 0.4926 (m100) REVERT: F 222 ASP cc_start: 0.8936 (m-30) cc_final: 0.8624 (m-30) REVERT: F 452 MET cc_start: 0.8244 (mmp) cc_final: 0.7451 (mmm) REVERT: F 624 MET cc_start: 0.8493 (ttm) cc_final: 0.7894 (tpt) REVERT: F 695 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.5360 (m-80) REVERT: I 71 ASN cc_start: 0.8660 (p0) cc_final: 0.8139 (p0) REVERT: I 85 PHE cc_start: 0.9123 (m-80) cc_final: 0.8716 (m-80) REVERT: I 86 TYR cc_start: 0.9022 (m-80) cc_final: 0.8399 (m-80) REVERT: I 104 MET cc_start: 0.8791 (mmm) cc_final: 0.8327 (tpp) REVERT: I 127 PHE cc_start: 0.9623 (t80) cc_final: 0.9410 (t80) REVERT: J 18 HIS cc_start: 0.6925 (t-170) cc_final: 0.6447 (t70) REVERT: J 102 THR cc_start: 0.5046 (t) cc_final: 0.4478 (t) REVERT: J 137 TYR cc_start: 0.6882 (m-10) cc_final: 0.6506 (m-80) REVERT: K 85 PHE cc_start: 0.9316 (m-80) cc_final: 0.8934 (m-80) REVERT: K 99 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9179 (mt) REVERT: K 133 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8565 (m-10) outliers start: 24 outliers final: 13 residues processed: 248 average time/residue: 0.1589 time to fit residues: 59.1338 Evaluate side-chains 209 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 156 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 173 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 40 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN D 110 HIS D 178 ASN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048189 restraints weight = 145747.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049478 restraints weight = 85836.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050287 restraints weight = 57947.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050909 restraints weight = 44439.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051300 restraints weight = 36951.308| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20855 Z= 0.143 Angle : 0.642 9.127 28183 Z= 0.340 Chirality : 0.044 0.431 3089 Planarity : 0.003 0.040 3493 Dihedral : 13.598 163.383 3140 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.52 % Allowed : 10.33 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2378 helix: 0.65 (0.15), residues: 1087 sheet: 0.56 (0.26), residues: 389 loop : -1.58 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 57 TYR 0.024 0.002 TYR I 126 PHE 0.052 0.002 PHE J 85 TRP 0.025 0.002 TRP F 339 HIS 0.010 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00301 (20854) covalent geometry : angle 0.64187 (28181) SS BOND : bond 0.00347 ( 1) SS BOND : angle 0.93612 ( 2) hydrogen bonds : bond 0.04175 ( 935) hydrogen bonds : angle 5.00219 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6489 (tt0) REVERT: E 157 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5875 (mtmm) REVERT: E 186 MET cc_start: 0.8975 (mmm) cc_final: 0.8430 (mpp) REVERT: E 201 PHE cc_start: 0.9434 (p90) cc_final: 0.8485 (p90) REVERT: E 259 PHE cc_start: 0.8911 (m-10) cc_final: 0.8691 (m-80) REVERT: F 184 TRP cc_start: 0.5379 (m100) cc_final: 0.4977 (m100) REVERT: F 228 ASN cc_start: 0.9184 (m-40) cc_final: 0.8913 (m-40) REVERT: F 452 MET cc_start: 0.8477 (mmp) cc_final: 0.7514 (mmm) REVERT: F 624 MET cc_start: 0.8411 (ttm) cc_final: 0.7880 (tpt) REVERT: F 695 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: H 13 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8637 (ptpp) REVERT: I 14 MET cc_start: 0.6800 (ttt) cc_final: 0.5325 (tmm) REVERT: I 16 PHE cc_start: 0.9188 (m-10) cc_final: 0.8837 (m-10) REVERT: I 85 PHE cc_start: 0.9145 (m-80) cc_final: 0.8647 (m-80) REVERT: I 104 MET cc_start: 0.8796 (mmm) cc_final: 0.8404 (tpp) REVERT: J 18 HIS cc_start: 0.6958 (t-170) cc_final: 0.6238 (t70) REVERT: J 136 TYR cc_start: 0.5508 (t80) cc_final: 0.5147 (t80) REVERT: K 14 MET cc_start: 0.1131 (mtm) cc_final: 0.0767 (mtm) REVERT: K 85 PHE cc_start: 0.9356 (m-80) cc_final: 0.9101 (m-80) REVERT: K 133 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8590 (m-10) outliers start: 33 outliers final: 17 residues processed: 229 average time/residue: 0.1589 time to fit residues: 54.8540 Evaluate side-chains 204 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 200 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS D 174 HIS F 155 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046009 restraints weight = 147959.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.047260 restraints weight = 87077.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048022 restraints weight = 59541.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.048393 restraints weight = 45989.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048943 restraints weight = 39110.064| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20855 Z= 0.151 Angle : 0.609 8.819 28183 Z= 0.324 Chirality : 0.042 0.221 3089 Planarity : 0.003 0.066 3493 Dihedral : 13.409 166.127 3140 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.43 % Allowed : 11.76 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2378 helix: 0.83 (0.16), residues: 1073 sheet: 0.58 (0.27), residues: 398 loop : -1.48 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 64 TYR 0.030 0.001 TYR J 126 PHE 0.046 0.002 PHE J 85 TRP 0.017 0.001 TRP F 339 HIS 0.014 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00318 (20854) covalent geometry : angle 0.60859 (28181) SS BOND : bond 0.00432 ( 1) SS BOND : angle 0.68460 ( 2) hydrogen bonds : bond 0.03880 ( 935) hydrogen bonds : angle 4.79249 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 157 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.6008 (mtmm) REVERT: E 259 PHE cc_start: 0.8807 (m-10) cc_final: 0.8495 (m-10) REVERT: F 184 TRP cc_start: 0.5558 (m100) cc_final: 0.5138 (m100) REVERT: F 222 ASP cc_start: 0.8935 (m-30) cc_final: 0.8644 (m-30) REVERT: F 452 MET cc_start: 0.8577 (mmp) cc_final: 0.7698 (mmm) REVERT: F 624 MET cc_start: 0.8384 (ttm) cc_final: 0.7937 (tpt) REVERT: F 695 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.5273 (m-80) REVERT: H 13 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8658 (ptpp) REVERT: I 85 PHE cc_start: 0.9096 (m-80) cc_final: 0.8706 (m-80) REVERT: I 104 MET cc_start: 0.9104 (mmm) cc_final: 0.8721 (tpp) REVERT: J 18 HIS cc_start: 0.6894 (t-170) cc_final: 0.6236 (t70) REVERT: J 136 TYR cc_start: 0.5687 (t80) cc_final: 0.5319 (t80) REVERT: J 137 TYR cc_start: 0.5942 (m-80) cc_final: 0.5565 (m-80) REVERT: K 85 PHE cc_start: 0.9441 (m-80) cc_final: 0.9067 (m-80) REVERT: K 124 CYS cc_start: 0.9736 (OUTLIER) cc_final: 0.9331 (m) REVERT: K 133 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8544 (m-10) outliers start: 31 outliers final: 16 residues processed: 212 average time/residue: 0.1497 time to fit residues: 49.0793 Evaluate side-chains 198 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 84 optimal weight: 0.0010 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 0.0980 chunk 233 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN F 43 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.060421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.046435 restraints weight = 147902.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047562 restraints weight = 88044.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.048354 restraints weight = 60741.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049012 restraints weight = 46085.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049278 restraints weight = 37651.792| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20855 Z= 0.161 Angle : 0.605 9.092 28183 Z= 0.320 Chirality : 0.042 0.236 3089 Planarity : 0.004 0.138 3493 Dihedral : 13.277 168.844 3140 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.43 % Allowed : 12.22 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2378 helix: 0.90 (0.16), residues: 1078 sheet: 0.58 (0.27), residues: 402 loop : -1.46 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 91 TYR 0.027 0.001 TYR K 80 PHE 0.023 0.002 PHE H 163 TRP 0.014 0.001 TRP F 339 HIS 0.012 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00341 (20854) covalent geometry : angle 0.60539 (28181) SS BOND : bond 0.00433 ( 1) SS BOND : angle 0.56206 ( 2) hydrogen bonds : bond 0.03740 ( 935) hydrogen bonds : angle 4.65613 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 MET cc_start: 0.9711 (mtp) cc_final: 0.9326 (mtm) REVERT: E 157 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.6091 (mtmm) REVERT: E 259 PHE cc_start: 0.8648 (m-10) cc_final: 0.8322 (m-10) REVERT: F 1 MET cc_start: 0.8317 (tpt) cc_final: 0.7566 (tpp) REVERT: F 184 TRP cc_start: 0.5789 (m100) cc_final: 0.5337 (m100) REVERT: F 452 MET cc_start: 0.8726 (mmp) cc_final: 0.7705 (mmm) REVERT: F 477 ARG cc_start: 0.9147 (mmt-90) cc_final: 0.8801 (mmp80) REVERT: F 624 MET cc_start: 0.8438 (ttm) cc_final: 0.7961 (tpt) REVERT: F 695 TYR cc_start: 0.5595 (OUTLIER) cc_final: 0.5008 (m-80) REVERT: H 13 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8709 (ptpp) REVERT: H 187 LEU cc_start: 0.9222 (mt) cc_final: 0.9018 (mm) REVERT: I 85 PHE cc_start: 0.9189 (m-80) cc_final: 0.8754 (m-80) REVERT: I 104 MET cc_start: 0.9180 (mmm) cc_final: 0.8692 (tpp) REVERT: J 18 HIS cc_start: 0.7158 (t-170) cc_final: 0.6512 (t70) REVERT: J 136 TYR cc_start: 0.6005 (t80) cc_final: 0.5613 (t80) REVERT: J 137 TYR cc_start: 0.6225 (m-80) cc_final: 0.5849 (m-80) REVERT: K 85 PHE cc_start: 0.9488 (m-80) cc_final: 0.9074 (m-80) REVERT: K 133 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8562 (m-10) outliers start: 31 outliers final: 15 residues processed: 201 average time/residue: 0.1430 time to fit residues: 44.4679 Evaluate side-chains 185 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 89 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 193 GLN D 72 HIS ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS E 86 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN I 27 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.056087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042518 restraints weight = 154129.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043620 restraints weight = 90857.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044137 restraints weight = 62501.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.044809 restraints weight = 49783.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045110 restraints weight = 41009.503| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 20855 Z= 0.402 Angle : 0.875 11.511 28183 Z= 0.458 Chirality : 0.048 0.201 3089 Planarity : 0.005 0.123 3493 Dihedral : 13.673 172.300 3140 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.40 % Allowed : 13.10 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.16), residues: 2378 helix: 0.32 (0.15), residues: 1065 sheet: 0.15 (0.26), residues: 414 loop : -1.64 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 64 TYR 0.032 0.003 TYR J 126 PHE 0.035 0.003 PHE F 442 TRP 0.016 0.002 TRP H 301 HIS 0.012 0.002 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00825 (20854) covalent geometry : angle 0.87529 (28181) SS BOND : bond 0.01570 ( 1) SS BOND : angle 1.17241 ( 2) hydrogen bonds : bond 0.04582 ( 935) hydrogen bonds : angle 5.26497 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 MET cc_start: 0.8394 (mmm) cc_final: 0.7749 (mpp) REVERT: E 259 PHE cc_start: 0.8207 (m-10) cc_final: 0.7801 (m-10) REVERT: F 184 TRP cc_start: 0.6128 (m100) cc_final: 0.5730 (m100) REVERT: F 452 MET cc_start: 0.8959 (mmp) cc_final: 0.7923 (mmm) REVERT: F 507 ASP cc_start: 0.5152 (OUTLIER) cc_final: 0.4760 (p0) REVERT: F 624 MET cc_start: 0.8264 (ttm) cc_final: 0.8046 (ttt) REVERT: F 695 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.5040 (m-80) REVERT: F 721 MET cc_start: 0.6869 (mtt) cc_final: 0.6058 (ttt) REVERT: H 17 HIS cc_start: 0.9200 (OUTLIER) cc_final: 0.8709 (t-90) REVERT: I 14 MET cc_start: 0.8127 (ttt) cc_final: 0.7761 (tpt) REVERT: I 37 GLN cc_start: 0.2949 (mt0) cc_final: 0.2413 (tm-30) REVERT: I 77 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8816 (mm-30) REVERT: I 85 PHE cc_start: 0.9216 (m-80) cc_final: 0.8735 (m-80) REVERT: I 104 MET cc_start: 0.9303 (mmm) cc_final: 0.8793 (tpp) REVERT: K 50 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8933 (p0) REVERT: K 85 PHE cc_start: 0.9478 (m-80) cc_final: 0.9229 (m-80) REVERT: K 133 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8636 (m-10) outliers start: 52 outliers final: 33 residues processed: 211 average time/residue: 0.1382 time to fit residues: 45.9083 Evaluate side-chains 200 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 507 ASP Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 17 HIS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 159 optimal weight: 0.0670 chunk 188 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS E 324 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.056868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043076 restraints weight = 147262.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044254 restraints weight = 86469.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045015 restraints weight = 59039.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045437 restraints weight = 45298.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045904 restraints weight = 38743.701| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20855 Z= 0.129 Angle : 0.636 10.355 28183 Z= 0.333 Chirality : 0.043 0.238 3089 Planarity : 0.004 0.099 3493 Dihedral : 13.402 169.968 3140 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.43 % Allowed : 14.39 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2378 helix: 0.89 (0.16), residues: 1063 sheet: 0.31 (0.26), residues: 401 loop : -1.45 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 64 TYR 0.026 0.001 TYR K 80 PHE 0.046 0.002 PHE J 85 TRP 0.013 0.001 TRP F 594 HIS 0.015 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00265 (20854) covalent geometry : angle 0.63599 (28181) SS BOND : bond 0.00086 ( 1) SS BOND : angle 1.16280 ( 2) hydrogen bonds : bond 0.03801 ( 935) hydrogen bonds : angle 4.69444 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9672 (OUTLIER) cc_final: 0.9414 (ttpp) REVERT: C 88 LYS cc_start: 0.8344 (mttt) cc_final: 0.8032 (mttp) REVERT: E 186 MET cc_start: 0.8467 (mmm) cc_final: 0.7826 (mpp) REVERT: E 188 LEU cc_start: 0.8526 (mp) cc_final: 0.8208 (tp) REVERT: E 259 PHE cc_start: 0.8441 (m-10) cc_final: 0.8066 (m-10) REVERT: E 327 MET cc_start: 0.9388 (ptm) cc_final: 0.9111 (pmm) REVERT: F 1 MET cc_start: 0.8554 (tpt) cc_final: 0.7738 (tpp) REVERT: F 184 TRP cc_start: 0.6246 (m100) cc_final: 0.5762 (m100) REVERT: F 222 ASP cc_start: 0.8985 (m-30) cc_final: 0.8714 (m-30) REVERT: F 259 MET cc_start: 0.9335 (mmm) cc_final: 0.8509 (mmm) REVERT: F 358 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8437 (t) REVERT: F 452 MET cc_start: 0.8846 (mmp) cc_final: 0.7693 (mmm) REVERT: F 477 ARG cc_start: 0.9167 (mmt-90) cc_final: 0.8809 (mmp80) REVERT: F 496 MET cc_start: 0.8030 (pmm) cc_final: 0.7762 (pmm) REVERT: F 507 ASP cc_start: 0.5351 (OUTLIER) cc_final: 0.5109 (p0) REVERT: F 695 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.4859 (m-80) REVERT: F 721 MET cc_start: 0.6719 (mtt) cc_final: 0.6210 (ttt) REVERT: I 14 MET cc_start: 0.7928 (ttt) cc_final: 0.7577 (tpt) REVERT: I 37 GLN cc_start: 0.2678 (mt0) cc_final: 0.2203 (tm-30) REVERT: I 85 PHE cc_start: 0.9152 (m-80) cc_final: 0.8681 (m-80) REVERT: I 96 ASP cc_start: 0.8163 (t0) cc_final: 0.7834 (m-30) REVERT: I 104 MET cc_start: 0.9204 (mmm) cc_final: 0.8682 (tpp) REVERT: K 85 PHE cc_start: 0.9502 (m-80) cc_final: 0.9229 (m-80) REVERT: K 133 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8602 (m-10) outliers start: 31 outliers final: 20 residues processed: 202 average time/residue: 0.1481 time to fit residues: 46.1209 Evaluate side-chains 187 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 507 ASP Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 94 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.043609 restraints weight = 150999.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.044746 restraints weight = 87469.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045457 restraints weight = 59388.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046011 restraints weight = 45945.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.046366 restraints weight = 38378.087| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20855 Z= 0.204 Angle : 0.655 10.280 28183 Z= 0.345 Chirality : 0.043 0.252 3089 Planarity : 0.004 0.090 3493 Dihedral : 13.338 171.703 3140 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.29 % Allowed : 15.54 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2378 helix: 0.90 (0.16), residues: 1064 sheet: 0.23 (0.26), residues: 406 loop : -1.46 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 64 TYR 0.034 0.002 TYR J 86 PHE 0.033 0.002 PHE J 85 TRP 0.013 0.001 TRP F 594 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00424 (20854) covalent geometry : angle 0.65479 (28181) SS BOND : bond 0.00665 ( 1) SS BOND : angle 0.82998 ( 2) hydrogen bonds : bond 0.03766 ( 935) hydrogen bonds : angle 4.72294 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9690 (OUTLIER) cc_final: 0.9420 (ttpp) REVERT: C 88 LYS cc_start: 0.8380 (mttt) cc_final: 0.8082 (mttp) REVERT: E 188 LEU cc_start: 0.8509 (mp) cc_final: 0.8237 (tp) REVERT: E 259 PHE cc_start: 0.8565 (m-10) cc_final: 0.8192 (m-10) REVERT: E 327 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.9167 (pmm) REVERT: F 1 MET cc_start: 0.8565 (tpt) cc_final: 0.7768 (tpp) REVERT: F 184 TRP cc_start: 0.6278 (m100) cc_final: 0.5821 (m100) REVERT: F 222 ASP cc_start: 0.9046 (m-30) cc_final: 0.8787 (m-30) REVERT: F 452 MET cc_start: 0.8859 (mmp) cc_final: 0.8039 (mmm) REVERT: F 496 MET cc_start: 0.8122 (pmm) cc_final: 0.7786 (pmm) REVERT: F 624 MET cc_start: 0.8548 (ttt) cc_final: 0.7904 (tpt) REVERT: F 665 ASP cc_start: 0.9328 (m-30) cc_final: 0.9086 (p0) REVERT: F 695 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.4682 (m-80) REVERT: F 721 MET cc_start: 0.6858 (mtt) cc_final: 0.6076 (ttt) REVERT: I 14 MET cc_start: 0.7998 (ttt) cc_final: 0.7612 (tpp) REVERT: I 37 GLN cc_start: 0.3079 (mt0) cc_final: 0.2519 (tm-30) REVERT: I 85 PHE cc_start: 0.9134 (m-80) cc_final: 0.8725 (m-80) REVERT: I 96 ASP cc_start: 0.8135 (t0) cc_final: 0.7870 (m-30) REVERT: I 104 MET cc_start: 0.9270 (mmm) cc_final: 0.8865 (tpp) REVERT: J 74 PHE cc_start: 0.7134 (p90) cc_final: 0.6910 (p90) REVERT: K 50 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8963 (p0) REVERT: K 85 PHE cc_start: 0.9493 (m-80) cc_final: 0.9244 (m-80) REVERT: K 123 TYR cc_start: 0.9401 (t80) cc_final: 0.9035 (t80) REVERT: K 133 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8581 (m-10) outliers start: 28 outliers final: 19 residues processed: 195 average time/residue: 0.1522 time to fit residues: 45.9149 Evaluate side-chains 189 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 102 optimal weight: 0.2980 chunk 151 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.057784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.044101 restraints weight = 149044.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.045220 restraints weight = 86354.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.046012 restraints weight = 59500.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.046356 restraints weight = 45471.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046854 restraints weight = 38873.509| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20855 Z= 0.140 Angle : 0.619 11.734 28183 Z= 0.324 Chirality : 0.043 0.273 3089 Planarity : 0.003 0.080 3493 Dihedral : 13.237 171.594 3140 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.25 % Allowed : 15.82 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2378 helix: 1.01 (0.16), residues: 1064 sheet: 0.24 (0.26), residues: 411 loop : -1.39 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 64 TYR 0.026 0.001 TYR K 80 PHE 0.048 0.002 PHE J 85 TRP 0.012 0.001 TRP F 594 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00296 (20854) covalent geometry : angle 0.61899 (28181) SS BOND : bond 0.00301 ( 1) SS BOND : angle 1.03506 ( 2) hydrogen bonds : bond 0.03595 ( 935) hydrogen bonds : angle 4.58934 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9670 (OUTLIER) cc_final: 0.9432 (ttpp) REVERT: C 88 LYS cc_start: 0.8340 (mttt) cc_final: 0.8060 (mttp) REVERT: E 125 ASN cc_start: 0.9076 (m-40) cc_final: 0.8699 (t0) REVERT: E 181 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7966 (mmmt) REVERT: E 188 LEU cc_start: 0.8453 (mp) cc_final: 0.8159 (tp) REVERT: E 259 PHE cc_start: 0.8636 (m-10) cc_final: 0.8191 (m-10) REVERT: E 327 MET cc_start: 0.9410 (ptm) cc_final: 0.9150 (pmm) REVERT: F 1 MET cc_start: 0.8576 (tpt) cc_final: 0.7704 (tpp) REVERT: F 8 MET cc_start: 0.9298 (mmp) cc_final: 0.8876 (mmp) REVERT: F 184 TRP cc_start: 0.6212 (m100) cc_final: 0.5716 (m100) REVERT: F 222 ASP cc_start: 0.9038 (m-30) cc_final: 0.8780 (m-30) REVERT: F 452 MET cc_start: 0.8799 (mmp) cc_final: 0.7978 (mmm) REVERT: F 477 ARG cc_start: 0.9193 (mmt-90) cc_final: 0.8841 (mmp80) REVERT: F 496 MET cc_start: 0.8080 (pmm) cc_final: 0.7733 (pmm) REVERT: F 624 MET cc_start: 0.8459 (ttt) cc_final: 0.7752 (tpt) REVERT: F 665 ASP cc_start: 0.9275 (m-30) cc_final: 0.9050 (p0) REVERT: F 695 TYR cc_start: 0.5391 (OUTLIER) cc_final: 0.4871 (m-80) REVERT: I 14 MET cc_start: 0.7898 (ttt) cc_final: 0.7523 (tpp) REVERT: I 59 TYR cc_start: 0.8709 (t80) cc_final: 0.8491 (t80) REVERT: I 77 GLU cc_start: 0.8883 (tp30) cc_final: 0.8678 (tm-30) REVERT: I 85 PHE cc_start: 0.9103 (m-80) cc_final: 0.8697 (m-80) REVERT: I 96 ASP cc_start: 0.8048 (t0) cc_final: 0.7801 (m-30) REVERT: I 104 MET cc_start: 0.9262 (mmm) cc_final: 0.8870 (tpp) REVERT: J 49 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7718 (ttm170) REVERT: K 85 PHE cc_start: 0.9520 (m-80) cc_final: 0.9235 (m-80) REVERT: K 133 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8535 (m-10) outliers start: 27 outliers final: 19 residues processed: 195 average time/residue: 0.1642 time to fit residues: 48.7160 Evaluate side-chains 187 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 187 optimal weight: 0.0770 chunk 65 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042172 restraints weight = 152536.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043307 restraints weight = 88600.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044004 restraints weight = 61596.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044322 restraints weight = 48241.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044827 restraints weight = 41607.763| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20855 Z= 0.161 Angle : 0.633 12.569 28183 Z= 0.331 Chirality : 0.043 0.423 3089 Planarity : 0.003 0.076 3493 Dihedral : 13.204 172.430 3140 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.20 % Allowed : 15.73 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2378 helix: 0.98 (0.16), residues: 1067 sheet: 0.25 (0.26), residues: 411 loop : -1.37 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 64 TYR 0.026 0.001 TYR J 86 PHE 0.035 0.002 PHE I 98 TRP 0.012 0.001 TRP F 594 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00339 (20854) covalent geometry : angle 0.63291 (28181) SS BOND : bond 0.00480 ( 1) SS BOND : angle 0.85629 ( 2) hydrogen bonds : bond 0.03604 ( 935) hydrogen bonds : angle 4.60937 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9670 (OUTLIER) cc_final: 0.9416 (ttpp) REVERT: C 88 LYS cc_start: 0.8372 (mttt) cc_final: 0.8164 (mttt) REVERT: E 125 ASN cc_start: 0.9077 (m-40) cc_final: 0.8698 (t0) REVERT: E 181 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8218 (mmmt) REVERT: E 188 LEU cc_start: 0.8415 (mp) cc_final: 0.8135 (tp) REVERT: E 259 PHE cc_start: 0.8671 (m-10) cc_final: 0.8287 (m-10) REVERT: E 327 MET cc_start: 0.9394 (ptm) cc_final: 0.9184 (ptt) REVERT: F 1 MET cc_start: 0.8558 (tpt) cc_final: 0.7725 (tpp) REVERT: F 184 TRP cc_start: 0.6204 (m100) cc_final: 0.5715 (m100) REVERT: F 222 ASP cc_start: 0.9022 (m-30) cc_final: 0.8767 (m-30) REVERT: F 288 MET cc_start: 0.9439 (tmm) cc_final: 0.9179 (ppp) REVERT: F 358 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8523 (t) REVERT: F 452 MET cc_start: 0.8766 (mmp) cc_final: 0.8024 (mmm) REVERT: F 477 ARG cc_start: 0.9168 (mmt-90) cc_final: 0.8786 (mmp80) REVERT: F 496 MET cc_start: 0.8060 (pmm) cc_final: 0.7705 (pmm) REVERT: F 624 MET cc_start: 0.8453 (ttt) cc_final: 0.7769 (tpt) REVERT: F 695 TYR cc_start: 0.5278 (OUTLIER) cc_final: 0.4732 (m-80) REVERT: I 14 MET cc_start: 0.7950 (ttt) cc_final: 0.7503 (tpp) REVERT: I 59 TYR cc_start: 0.8776 (t80) cc_final: 0.8567 (t80) REVERT: I 85 PHE cc_start: 0.9057 (m-80) cc_final: 0.8676 (m-80) REVERT: I 96 ASP cc_start: 0.7987 (t0) cc_final: 0.7785 (m-30) REVERT: I 104 MET cc_start: 0.9267 (mmm) cc_final: 0.8706 (tpp) REVERT: J 53 GLU cc_start: 0.9284 (pt0) cc_final: 0.9063 (tm-30) REVERT: K 85 PHE cc_start: 0.9517 (m-80) cc_final: 0.9237 (m-80) REVERT: K 123 TYR cc_start: 0.9379 (t80) cc_final: 0.9027 (t80) REVERT: K 133 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (m-10) outliers start: 26 outliers final: 21 residues processed: 184 average time/residue: 0.1588 time to fit residues: 44.4381 Evaluate side-chains 188 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 54 GLN Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 135 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042171 restraints weight = 151687.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043315 restraints weight = 87766.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044029 restraints weight = 60290.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044537 restraints weight = 47057.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044891 restraints weight = 39464.791| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20855 Z= 0.159 Angle : 0.636 12.975 28183 Z= 0.331 Chirality : 0.043 0.324 3089 Planarity : 0.003 0.072 3493 Dihedral : 13.194 172.714 3140 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.34 % Allowed : 15.96 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2378 helix: 1.01 (0.16), residues: 1065 sheet: 0.24 (0.26), residues: 411 loop : -1.36 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 64 TYR 0.027 0.001 TYR J 86 PHE 0.025 0.002 PHE J 85 TRP 0.012 0.001 TRP F 594 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00336 (20854) covalent geometry : angle 0.63594 (28181) SS BOND : bond 0.00440 ( 1) SS BOND : angle 0.83843 ( 2) hydrogen bonds : bond 0.03612 ( 935) hydrogen bonds : angle 4.57168 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3530.59 seconds wall clock time: 62 minutes 7.28 seconds (3727.28 seconds total)