Starting phenix.real_space_refine on Sun Sep 13 04:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v00_26924/09_2026/7v00_26924_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v00_26924/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v00_26924/09_2026/7v00_26924_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v00_26924/09_2026/7v00_26924_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v00_26924/09_2026/7v00_26924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v00_26924/09_2026/7v00_26924.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.69, per 1000 atoms: 0.23 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: 1.52 Conformation dependent library (CDL) restraints added in 708.1 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: 2.05 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: 3.02 Time building geometry restraints manager: 1.93 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 1.483 1.386 0.097 1.50e-02 4.44e+03 4.16e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.483 1.567 -0.084 1.50e-02 4.44e+03 3.10e+01 bond pdb=" C1' C G 28 " pdb=" N1 C G 28 " ideal model delta sigma weight residual 1.483 1.565 -0.082 1.50e-02 4.44e+03 2.97e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.483 1.402 0.081 1.50e-02 4.44e+03 2.93e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.464 1.540 -0.076 1.40e-02 5.10e+03 2.93e+01 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27236 2.13 - 4.27: 791 4.27 - 6.40: 130 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=" O5' G G 20 " pdb=" C5' G G 20 " pdb=" C4' G G 20 " ideal model delta sigma weight residual 109.40 113.32 -3.92 8.00e-01 1.56e+00 2.40e+01 angle pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sigma weight residual 118.80 124.06 -5.26 1.10e+00 8.26e-01 2.29e+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: 2484 0.066 - 0.132: 540 0.132 - 0.198: 54 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: 6.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.880 Find NCS groups from input model: 0.190 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: 0.010 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: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 0.097 20855 Z= 0.349 Angle : 0.869 10.663 28183 Z= 0.529 Chirality : 0.054 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/Z covalent geometry : bond 0.00591 / 0.35 (20854) covalent geometry : angle 0.86893 / 0.53 (28181) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 1.35683 / 0.72 ( 2) hydrogen bonds : bond 0.18188 / 12.43 ( 935) hydrogen bonds : angle 7.14156 / 5.01 ( 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 : 0.776 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: 0.7391 (p) REVERT: E 28 ASP cc_start: 0.8385 (m-30) cc_final: 0.7785 (m-30) REVERT: E 33 PHE cc_start: 0.8218 (m-10) cc_final: 0.7707 (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: 0.7513 (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: 0.6670 (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: 0.8043 (m110) outliers start: 7 outliers final: 0 residues processed: 449 average time/residue: 0.1746 time to fit residues: 114.0471 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 : 0.774 ------------------------------------------------------------------------------- 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... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** 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 178 ASN E 60 GLN E 316 ASN E 324 GLN F 14 HIS ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 482 ASN F 560 GLN F 708 ASN H 87 HIS ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.061782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.047667 restraints weight = 144788.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049015 restraints weight = 83378.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.049847 restraints weight = 56157.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.050495 restraints weight = 42799.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.050889 restraints weight = 35290.579| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20855 Z= 0.176 Angle : 0.778 15.289 28183 Z= 0.413 Chirality : 0.048 0.321 3089 Planarity : 0.004 0.062 3493 Dihedral : 13.932 165.833 3140 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.38 % Allowed : 9.73 % Favored : 88.88 % 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: -0.61 (0.17), residues: 2378 helix: 0.39 (0.15), residues: 1080 sheet: 0.33 (0.26), residues: 391 loop : -1.68 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 64 TYR 0.034 0.002 TYR D 180 PHE 0.028 0.002 PHE I 85 TRP 0.038 0.002 TRP F 339 HIS 0.010 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (20854) covalent geometry : angle 0.77759 / 0.41 (28181) SS BOND : bond 0.00640 / 0.34 ( 1) SS BOND : angle 1.67992 / 0.88 ( 2) hydrogen bonds : bond 0.05487 / 3.76 ( 935) hydrogen bonds : angle 5.62827 / 3.91 ( 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 264 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.795 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: D 67 MET cc_start: 0.8350 (tmm) cc_final: 0.8026 (tmm) REVERT: E 28 ASP cc_start: 0.8739 (m-30) cc_final: 0.8308 (t0) REVERT: E 157 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5861 (mtmm) REVERT: E 186 MET cc_start: 0.8514 (mmm) cc_final: 0.7876 (mpp) REVERT: E 259 PHE cc_start: 0.7795 (m-10) cc_final: 0.7394 (m-10) REVERT: F 1 MET cc_start: 0.8093 (mmt) cc_final: 0.7720 (mmt) REVERT: F 184 TRP cc_start: 0.5628 (m100) cc_final: 0.5022 (m100) REVERT: F 222 ASP cc_start: 0.8906 (m-30) cc_final: 0.8385 (m-30) REVERT: F 452 MET cc_start: 0.8085 (mmp) cc_final: 0.7359 (mmm) REVERT: F 477 ARG cc_start: 0.8987 (mmt-90) cc_final: 0.8716 (mmp80) REVERT: F 624 MET cc_start: 0.8483 (ttm) cc_final: 0.7834 (tpt) REVERT: F 695 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: H 187 LEU cc_start: 0.9064 (mt) cc_final: 0.8823 (mm) REVERT: I 71 ASN cc_start: 0.8639 (p0) cc_final: 0.8101 (p0) REVERT: I 85 PHE cc_start: 0.9132 (m-80) cc_final: 0.8639 (m-80) REVERT: I 97 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: I 104 MET cc_start: 0.8803 (mmm) cc_final: 0.8413 (tpp) REVERT: J 18 HIS cc_start: 0.6696 (t-170) cc_final: 0.6179 (t70) REVERT: J 78 LEU cc_start: 0.9291 (mt) cc_final: 0.9068 (tp) REVERT: J 137 TYR cc_start: 0.6481 (m-10) cc_final: 0.5966 (m-80) REVERT: K 133 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8584 (m-10) outliers start: 30 outliers final: 16 residues processed: 257 average time/residue: 0.1554 time to fit residues: 60.2172 Evaluate side-chains 214 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 157 LYS 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 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 182 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 60 THR 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: 3.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 10 optimal weight: 0.0170 chunk 173 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN D 110 HIS D 178 ASN F 38 HIS F 155 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** 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 = 0.3486 r_free = 0.3486 target = 0.060726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046598 restraints weight = 146308.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047841 restraints weight = 87019.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048632 restraints weight = 59947.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049286 restraints weight = 46160.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049667 restraints weight = 37898.536| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20855 Z= 0.169 Angle : 0.683 9.292 28183 Z= 0.366 Chirality : 0.044 0.193 3089 Planarity : 0.004 0.043 3493 Dihedral : 13.732 168.186 3140 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.48 % Allowed : 10.24 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2378 helix: 0.56 (0.15), residues: 1084 sheet: 0.39 (0.26), residues: 390 loop : -1.56 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 64 TYR 0.020 0.002 TYR J 123 PHE 0.035 0.002 PHE J 119 TRP 0.023 0.002 TRP F 339 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (20854) covalent geometry : angle 0.68331 / 0.37 (28181) SS BOND : bond 0.00474 / 0.25 ( 1) SS BOND : angle 1.11922 / 0.59 ( 2) hydrogen bonds : bond 0.04745 / 3.27 ( 935) hydrogen bonds : angle 5.28228 / 3.66 ( 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 226 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.860 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: E 28 ASP cc_start: 0.8751 (m-30) cc_final: 0.8480 (t0) REVERT: E 186 MET cc_start: 0.8819 (mmm) cc_final: 0.8234 (mpp) REVERT: E 259 PHE cc_start: 0.8716 (m-10) cc_final: 0.8393 (m-10) REVERT: E 327 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9256 (pmm) REVERT: F 184 TRP cc_start: 0.5340 (m100) cc_final: 0.5007 (m100) REVERT: F 222 ASP cc_start: 0.8941 (m-30) cc_final: 0.8616 (m-30) REVERT: F 288 MET cc_start: 0.8791 (tmm) cc_final: 0.8492 (tmm) REVERT: F 452 MET cc_start: 0.8247 (mmp) cc_final: 0.7455 (mmm) REVERT: F 624 MET cc_start: 0.8466 (ttm) cc_final: 0.7886 (tpt) REVERT: F 695 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: I 85 PHE cc_start: 0.9171 (m-80) cc_final: 0.8752 (m-80) REVERT: I 104 MET cc_start: 0.9061 (mmm) cc_final: 0.8695 (tpp) REVERT: I 119 PHE cc_start: 0.9421 (t80) cc_final: 0.9092 (t80) REVERT: J 18 HIS cc_start: 0.6747 (t-170) cc_final: 0.6225 (t70) REVERT: J 137 TYR cc_start: 0.6718 (m-10) cc_final: 0.6235 (m-80) REVERT: K 123 TYR cc_start: 0.9446 (t80) cc_final: 0.9242 (t80) REVERT: K 133 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8609 (m-10) outliers start: 32 outliers final: 17 residues processed: 218 average time/residue: 0.1582 time to fit residues: 52.8346 Evaluate side-chains 201 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 40 MET Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 327 MET 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 182 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 95 VAL 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: 6.9990 chunk 238 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.0370 chunk 211 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.060945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.046861 restraints weight = 145854.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.048136 restraints weight = 86587.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048927 restraints weight = 59224.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049560 restraints weight = 45403.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.049971 restraints weight = 37256.597| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20855 Z= 0.132 Angle : 0.644 10.116 28183 Z= 0.339 Chirality : 0.044 0.539 3089 Planarity : 0.003 0.038 3493 Dihedral : 13.552 170.325 3140 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.38 % Allowed : 11.58 % Favored : 87.04 % 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: -0.28 (0.17), residues: 2378 helix: 0.67 (0.16), residues: 1085 sheet: 0.51 (0.27), residues: 384 loop : -1.53 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 64 TYR 0.031 0.002 TYR J 126 PHE 0.052 0.002 PHE J 85 TRP 0.018 0.001 TRP F 339 HIS 0.019 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20854) covalent geometry : angle 0.64407 / 0.34 (28181) SS BOND : bond 0.00203 / 0.11 ( 1) SS BOND : angle 0.92921 / 0.51 ( 2) hydrogen bonds : bond 0.04235 / 2.88 ( 935) hydrogen bonds : angle 4.97740 / 3.44 ( 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 216 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.829 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 186 MET cc_start: 0.8913 (mmm) cc_final: 0.8352 (mpp) REVERT: E 259 PHE cc_start: 0.8665 (m-10) cc_final: 0.8424 (m-10) REVERT: E 327 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9293 (pmm) REVERT: F 184 TRP cc_start: 0.5346 (m100) cc_final: 0.4951 (m100) REVERT: F 222 ASP cc_start: 0.8969 (m-30) cc_final: 0.8644 (m-30) REVERT: F 288 MET cc_start: 0.8973 (tmm) cc_final: 0.8621 (tmm) REVERT: F 452 MET cc_start: 0.8361 (mmp) cc_final: 0.7345 (mmm) REVERT: F 624 MET cc_start: 0.8384 (ttm) cc_final: 0.7901 (tpt) REVERT: F 695 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5298 (m-80) REVERT: I 85 PHE cc_start: 0.9132 (m-80) cc_final: 0.8739 (m-80) REVERT: I 86 TYR cc_start: 0.8930 (m-80) cc_final: 0.8190 (m-80) REVERT: I 104 MET cc_start: 0.9112 (mmm) cc_final: 0.8595 (tpp) REVERT: I 119 PHE cc_start: 0.9392 (t80) cc_final: 0.9039 (t80) REVERT: J 18 HIS cc_start: 0.6692 (t-170) cc_final: 0.6248 (t70) REVERT: J 107 ILE cc_start: 0.7723 (mm) cc_final: 0.7450 (mm) REVERT: J 136 TYR cc_start: 0.5635 (t80) cc_final: 0.5430 (t80) REVERT: K 133 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8587 (m-10) outliers start: 30 outliers final: 13 residues processed: 208 average time/residue: 0.1542 time to fit residues: 49.5259 Evaluate side-chains 193 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 327 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 167 LEU 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 J residue 45 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 121 LEU 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: 0.0970 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.059396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.045567 restraints weight = 148773.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046811 restraints weight = 87941.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.047552 restraints weight = 59746.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048134 restraints weight = 46127.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048532 restraints weight = 37980.002| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20855 Z= 0.184 Angle : 0.636 10.010 28183 Z= 0.337 Chirality : 0.043 0.224 3089 Planarity : 0.003 0.038 3493 Dihedral : 13.405 172.710 3140 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.48 % Allowed : 12.13 % Favored : 86.39 % 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: -0.15 (0.17), residues: 2378 helix: 0.78 (0.16), residues: 1077 sheet: 0.54 (0.27), residues: 390 loop : -1.45 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 190 TYR 0.024 0.002 TYR K 123 PHE 0.027 0.002 PHE J 85 TRP 0.017 0.001 TRP F 339 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (20854) covalent geometry : angle 0.63599 / 0.34 (28181) SS BOND : bond 0.00673 / 0.35 ( 1) SS BOND : angle 0.75304 / 0.40 ( 2) hydrogen bonds : bond 0.03963 / 2.69 ( 935) hydrogen bonds : angle 4.85754 / 3.36 ( 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: 32 poor density : 177 time to evaluate : 0.718 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: C 55 MET cc_start: 0.9700 (mtp) cc_final: 0.9308 (mtm) REVERT: E 259 PHE cc_start: 0.8583 (m-10) cc_final: 0.8334 (m-10) REVERT: E 327 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9230 (pmm) REVERT: F 1 MET cc_start: 0.8199 (tpt) cc_final: 0.7490 (tpp) REVERT: F 184 TRP cc_start: 0.5545 (m100) cc_final: 0.5133 (m100) REVERT: F 222 ASP cc_start: 0.8945 (m-30) cc_final: 0.8652 (m-30) REVERT: F 288 MET cc_start: 0.9082 (tmm) cc_final: 0.8876 (tmm) REVERT: F 343 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: F 452 MET cc_start: 0.8555 (mmp) cc_final: 0.7522 (mmm) REVERT: F 624 MET cc_start: 0.8435 (ttm) cc_final: 0.8004 (tpt) REVERT: F 695 TYR cc_start: 0.5838 (OUTLIER) cc_final: 0.5211 (m-80) REVERT: I 14 MET cc_start: 0.7272 (ttt) cc_final: 0.6817 (tpp) REVERT: I 85 PHE cc_start: 0.9182 (m-80) cc_final: 0.8765 (m-80) REVERT: I 86 TYR cc_start: 0.8940 (m-80) cc_final: 0.8114 (m-80) REVERT: I 96 ASP cc_start: 0.8060 (t0) cc_final: 0.7794 (m-30) REVERT: I 104 MET cc_start: 0.9103 (mmm) cc_final: 0.8632 (tpp) REVERT: J 18 HIS cc_start: 0.6962 (t-170) cc_final: 0.6473 (t70) REVERT: J 85 PHE cc_start: 0.7754 (m-80) cc_final: 0.7546 (m-80) REVERT: K 133 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8565 (m-10) outliers start: 32 outliers final: 16 residues processed: 200 average time/residue: 0.1421 time to fit residues: 44.5245 Evaluate side-chains 185 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 327 MET 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 343 GLU Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 121 LEU 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: 10.0000 chunk 224 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 179 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 163 optimal weight: 0.0040 chunk 118 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.059036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.045170 restraints weight = 148393.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046349 restraints weight = 87984.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.047143 restraints weight = 60532.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047723 restraints weight = 46616.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.048104 restraints weight = 38593.426| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20855 Z= 0.175 Angle : 0.625 10.858 28183 Z= 0.330 Chirality : 0.043 0.399 3089 Planarity : 0.004 0.163 3493 Dihedral : 13.345 173.418 3140 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.34 % Allowed : 13.05 % Favored : 85.61 % 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: -0.08 (0.17), residues: 2378 helix: 0.87 (0.16), residues: 1065 sheet: 0.50 (0.27), residues: 402 loop : -1.40 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 190 TYR 0.029 0.002 TYR J 126 PHE 0.021 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/Z covalent geometry : bond 0.00374 / 0.17 (20854) covalent geometry : angle 0.62539 / 0.33 (28181) SS BOND : bond 0.00530 / 0.28 ( 1) SS BOND : angle 0.68214 / 0.36 ( 2) hydrogen bonds : bond 0.03867 / 2.62 ( 935) hydrogen bonds : angle 4.80201 / 3.32 ( 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 200 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.732 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: E 327 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.9219 (pmm) REVERT: F 184 TRP cc_start: 0.5644 (m100) cc_final: 0.5240 (m100) REVERT: F 222 ASP cc_start: 0.8925 (m-30) cc_final: 0.8647 (m-30) REVERT: F 288 MET cc_start: 0.9174 (tmm) cc_final: 0.8905 (tmm) REVERT: F 343 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: F 452 MET cc_start: 0.8533 (mmp) cc_final: 0.7512 (mmm) REVERT: F 695 TYR cc_start: 0.5784 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: I 14 MET cc_start: 0.7428 (ttt) cc_final: 0.6987 (tpp) REVERT: I 85 PHE cc_start: 0.9182 (m-80) cc_final: 0.8812 (m-80) REVERT: I 86 TYR cc_start: 0.8985 (m-80) cc_final: 0.8215 (m-80) REVERT: I 104 MET cc_start: 0.9129 (mmm) cc_final: 0.8695 (tpp) REVERT: J 18 HIS cc_start: 0.6957 (t-90) cc_final: 0.6450 (t70) REVERT: K 85 PHE cc_start: 0.9541 (m-80) cc_final: 0.9126 (m-80) REVERT: K 133 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8590 (m-10) outliers start: 29 outliers final: 16 residues processed: 194 average time/residue: 0.1404 time to fit residues: 42.4591 Evaluate side-chains 189 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 142 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 327 MET 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 343 GLU Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR 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 J residue 83 ILE 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: 0.2980 chunk 188 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS H 251 GLN ** 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 = 0.3423 r_free = 0.3423 target = 0.057788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.044083 restraints weight = 149158.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.045224 restraints weight = 88141.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045981 restraints weight = 61102.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.046587 restraints weight = 46935.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046975 restraints weight = 38413.186| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20855 Z= 0.207 Angle : 0.658 13.599 28183 Z= 0.347 Chirality : 0.044 0.248 3089 Planarity : 0.004 0.135 3493 Dihedral : 13.296 174.275 3140 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.48 % Allowed : 13.70 % Favored : 84.82 % 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: -0.08 (0.17), residues: 2378 helix: 0.94 (0.16), residues: 1057 sheet: 0.39 (0.27), residues: 409 loop : -1.42 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 64 TYR 0.019 0.002 TYR H 184 PHE 0.030 0.002 PHE K 98 TRP 0.012 0.001 TRP F 339 HIS 0.011 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (20854) covalent geometry : angle 0.65790 / 0.35 (28181) SS BOND : bond 0.00662 / 0.35 ( 1) SS BOND : angle 0.66696 / 0.36 ( 2) hydrogen bonds : bond 0.03866 / 2.62 ( 935) hydrogen bonds : angle 4.81707 / 3.34 ( 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: 32 poor density : 176 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: A 171 LYS cc_start: 0.9717 (OUTLIER) cc_final: 0.9401 (ttpp) REVERT: C 55 MET cc_start: 0.9709 (mtp) cc_final: 0.9327 (mpp) REVERT: D 167 GLU cc_start: 0.9490 (tt0) cc_final: 0.9286 (tp30) REVERT: E 24 MET cc_start: 0.7496 (mmp) cc_final: 0.6597 (tpt) REVERT: F 184 TRP cc_start: 0.5865 (m100) cc_final: 0.5406 (m100) REVERT: F 343 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: F 452 MET cc_start: 0.8634 (mmp) cc_final: 0.7648 (mmm) REVERT: F 624 MET cc_start: 0.8367 (ttm) cc_final: 0.7882 (tpt) REVERT: F 695 TYR cc_start: 0.5544 (OUTLIER) cc_final: 0.4876 (m-80) REVERT: I 85 PHE cc_start: 0.9226 (m-80) cc_final: 0.8853 (m-80) REVERT: I 86 TYR cc_start: 0.9024 (m-80) cc_final: 0.8347 (m-80) REVERT: I 96 ASP cc_start: 0.8013 (t0) cc_final: 0.7764 (m-30) REVERT: I 104 MET cc_start: 0.9119 (mmm) cc_final: 0.8759 (tpp) REVERT: K 85 PHE cc_start: 0.9545 (m-80) cc_final: 0.9048 (m-80) REVERT: K 123 TYR cc_start: 0.9398 (t80) cc_final: 0.9019 (t80) REVERT: K 133 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8569 (m-10) outliers start: 32 outliers final: 22 residues processed: 200 average time/residue: 0.1471 time to fit residues: 45.9809 Evaluate side-chains 194 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 142 VAL 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 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR 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 I residue 77 GLU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 121 LEU 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: 8.9990 chunk 38 optimal weight: 0.0020 chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.057570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043836 restraints weight = 150939.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.045001 restraints weight = 88801.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045767 restraints weight = 60907.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.046339 restraints weight = 46933.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046697 restraints weight = 38851.095| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20855 Z= 0.198 Angle : 0.655 10.902 28183 Z= 0.344 Chirality : 0.043 0.237 3089 Planarity : 0.004 0.124 3493 Dihedral : 13.256 174.608 3140 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.43 % Allowed : 13.84 % Favored : 84.73 % 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: 0.97 (0.16), residues: 1060 sheet: 0.37 (0.27), residues: 403 loop : -1.40 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 190 TYR 0.037 0.002 TYR J 86 PHE 0.017 0.002 PHE K 16 TRP 0.009 0.001 TRP F 594 HIS 0.012 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (20854) covalent geometry : angle 0.65542 / 0.34 (28181) SS BOND : bond 0.00616 / 0.32 ( 1) SS BOND : angle 0.70862 / 0.38 ( 2) hydrogen bonds : bond 0.03807 / 2.57 ( 935) hydrogen bonds : angle 4.78759 / 3.34 ( 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 206 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.696 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: A 171 LYS cc_start: 0.9716 (OUTLIER) cc_final: 0.9398 (ttpp) REVERT: D 167 GLU cc_start: 0.9485 (tt0) cc_final: 0.9278 (tp30) REVERT: E 92 PHE cc_start: 0.5569 (m-10) cc_final: 0.5254 (m-80) REVERT: F 1 MET cc_start: 0.8316 (tpt) cc_final: 0.7597 (tpp) REVERT: F 184 TRP cc_start: 0.5958 (m100) cc_final: 0.5507 (m100) REVERT: F 343 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: F 452 MET cc_start: 0.8720 (mmp) cc_final: 0.7776 (mmm) REVERT: F 477 ARG cc_start: 0.9167 (mmt-90) cc_final: 0.8810 (mmp80) REVERT: F 695 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.4844 (m-80) REVERT: I 14 MET cc_start: 0.7414 (ttm) cc_final: 0.7146 (tpp) REVERT: I 85 PHE cc_start: 0.9178 (m-80) cc_final: 0.8753 (m-80) REVERT: I 96 ASP cc_start: 0.7829 (t0) cc_final: 0.7564 (m-30) REVERT: K 85 PHE cc_start: 0.9573 (m-80) cc_final: 0.9333 (m-80) REVERT: K 133 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8584 (m-10) outliers start: 31 outliers final: 23 residues processed: 198 average time/residue: 0.1526 time to fit residues: 46.5665 Evaluate side-chains 193 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 142 VAL 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 343 GLU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP 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 I residue 122 ASP Chi-restraints excluded: chain J residue 45 THR 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 133 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 102 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 225 optimal weight: 0.0270 chunk 126 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.058133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044341 restraints weight = 146925.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045571 restraints weight = 85912.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046328 restraints weight = 58856.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046884 restraints weight = 45699.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047251 restraints weight = 38150.846| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20855 Z= 0.129 Angle : 0.625 11.391 28183 Z= 0.327 Chirality : 0.043 0.245 3089 Planarity : 0.004 0.113 3493 Dihedral : 13.137 174.713 3140 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.38 % Allowed : 14.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.07 (0.16), residues: 1066 sheet: 0.34 (0.26), residues: 410 loop : -1.35 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 190 TYR 0.021 0.001 TYR H 184 PHE 0.025 0.002 PHE J 120 TRP 0.011 0.001 TRP E 89 HIS 0.019 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (20854) covalent geometry : angle 0.62545 / 0.33 (28181) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 0.87525 / 0.47 ( 2) hydrogen bonds : bond 0.03682 / 2.49 ( 935) hydrogen bonds : angle 4.64708 / 3.23 ( 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 204 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.798 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: A 171 LYS cc_start: 0.9708 (OUTLIER) cc_final: 0.9413 (ttpp) REVERT: C 55 MET cc_start: 0.9702 (mtp) cc_final: 0.9303 (mpp) REVERT: C 88 LYS cc_start: 0.8363 (mttt) cc_final: 0.7983 (mptt) REVERT: D 167 GLU cc_start: 0.9464 (tt0) cc_final: 0.9257 (tp30) REVERT: E 92 PHE cc_start: 0.5536 (m-10) cc_final: 0.5311 (m-80) REVERT: F 1 MET cc_start: 0.8368 (tpt) cc_final: 0.7648 (tpp) REVERT: F 8 MET cc_start: 0.9242 (mmp) cc_final: 0.8801 (mmp) REVERT: F 184 TRP cc_start: 0.5954 (m100) cc_final: 0.5483 (m100) REVERT: F 222 ASP cc_start: 0.8955 (m-30) cc_final: 0.8680 (m-30) REVERT: F 452 MET cc_start: 0.8660 (mmp) cc_final: 0.7672 (mmm) REVERT: F 624 MET cc_start: 0.8391 (ttm) cc_final: 0.7748 (ttt) REVERT: F 695 TYR cc_start: 0.5270 (OUTLIER) cc_final: 0.4663 (m-80) REVERT: I 85 PHE cc_start: 0.9133 (m-80) cc_final: 0.8719 (m-80) REVERT: I 96 ASP cc_start: 0.7839 (t0) cc_final: 0.7594 (m-30) REVERT: I 104 MET cc_start: 0.9052 (mmm) cc_final: 0.8630 (tpp) REVERT: K 85 PHE cc_start: 0.9596 (m-80) cc_final: 0.9359 (m-80) REVERT: K 123 TYR cc_start: 0.9375 (t80) cc_final: 0.9019 (t80) REVERT: K 133 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8588 (m-10) outliers start: 30 outliers final: 21 residues processed: 198 average time/residue: 0.1441 time to fit residues: 44.5945 Evaluate side-chains 191 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 E residue 23 VAL Chi-restraints excluded: chain E residue 57 TYR 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 117 VAL 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 443 VAL Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR 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 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: 4.9990 chunk 5 optimal weight: 4.9990 chunk 187 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.058487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.044896 restraints weight = 147568.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.046100 restraints weight = 85844.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046872 restraints weight = 58576.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047481 restraints weight = 44656.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047850 restraints weight = 36765.916| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20855 Z= 0.119 Angle : 0.639 13.271 28183 Z= 0.332 Chirality : 0.044 0.412 3089 Planarity : 0.004 0.105 3493 Dihedral : 12.989 175.386 3140 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.06 % Allowed : 15.22 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.11 (0.17), residues: 2378 helix: 1.09 (0.16), residues: 1063 sheet: 0.39 (0.26), residues: 409 loop : -1.29 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 64 TYR 0.024 0.001 TYR K 80 PHE 0.034 0.001 PHE I 98 TRP 0.014 0.001 TRP F 339 HIS 0.012 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (20854) covalent geometry : angle 0.63899 / 0.33 (28181) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 1.02272 / 0.56 ( 2) hydrogen bonds : bond 0.03610 / 2.43 ( 935) hydrogen bonds : angle 4.60609 / 3.20 ( 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: 23 poor density : 166 time to evaluate : 0.797 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: A 171 LYS cc_start: 0.9703 (OUTLIER) cc_final: 0.9442 (ttpp) REVERT: C 55 MET cc_start: 0.9713 (mtp) cc_final: 0.9323 (mpp) REVERT: C 88 LYS cc_start: 0.8270 (mttt) cc_final: 0.7913 (mptt) REVERT: E 92 PHE cc_start: 0.5749 (m-10) cc_final: 0.5447 (m-80) REVERT: F 1 MET cc_start: 0.8405 (tpt) cc_final: 0.7647 (tpp) REVERT: F 184 TRP cc_start: 0.5901 (m100) cc_final: 0.5474 (m100) REVERT: F 222 ASP cc_start: 0.8972 (m-30) cc_final: 0.8697 (m-30) REVERT: F 452 MET cc_start: 0.8663 (mmp) cc_final: 0.7673 (mmm) REVERT: F 496 MET cc_start: 0.8072 (pmm) cc_final: 0.7830 (pmm) REVERT: F 624 MET cc_start: 0.8300 (ttm) cc_final: 0.7593 (ttt) REVERT: F 634 MET cc_start: 0.9305 (tpp) cc_final: 0.8942 (tpt) REVERT: F 695 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4544 (m-80) REVERT: I 85 PHE cc_start: 0.9126 (m-80) cc_final: 0.8693 (m-80) REVERT: I 96 ASP cc_start: 0.7700 (t0) cc_final: 0.7441 (m-30) REVERT: I 104 MET cc_start: 0.9090 (mmm) cc_final: 0.8678 (tpp) REVERT: K 85 PHE cc_start: 0.9614 (m-80) cc_final: 0.9366 (m-80) REVERT: K 123 TYR cc_start: 0.9374 (t80) cc_final: 0.9020 (t80) REVERT: K 133 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8584 (m-10) outliers start: 23 outliers final: 19 residues processed: 186 average time/residue: 0.1545 time to fit residues: 44.2340 Evaluate side-chains 186 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 432 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 471 GLN Chi-restraints excluded: chain F residue 498 ASP 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 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: 2.9990 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 214 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 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 = 0.3433 r_free = 0.3433 target = 0.057906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044319 restraints weight = 149266.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.045564 restraints weight = 86349.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046298 restraints weight = 58386.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.046840 restraints weight = 45205.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047159 restraints weight = 37944.431| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5432 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= 0.147 Angle : 0.637 11.306 28183 Z= 0.332 Chirality : 0.043 0.258 3089 Planarity : 0.004 0.100 3493 Dihedral : 12.919 175.994 3140 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.01 % Allowed : 15.31 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.09 (0.17), residues: 2378 helix: 1.04 (0.16), residues: 1079 sheet: 0.40 (0.26), residues: 408 loop : -1.31 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 190 TYR 0.018 0.001 TYR I 123 PHE 0.031 0.001 PHE E 62 TRP 0.011 0.001 TRP F 339 HIS 0.012 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (20854) covalent geometry : angle 0.63675 / 0.33 (28181) SS BOND : bond 0.00338 / 0.18 ( 1) SS BOND : angle 0.76967 / 0.41 ( 2) hydrogen bonds : bond 0.03603 / 2.45 ( 935) hydrogen bonds : angle 4.60543 / 3.20 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.63 seconds wall clock time: 60 minutes 16.44 seconds (3616.44 seconds total)