Starting phenix.real_space_refine on Wed Jun 18 05:12:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v00_26924/06_2025/7v00_26924_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v00_26924/06_2025/7v00_26924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v00_26924/06_2025/7v00_26924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v00_26924/06_2025/7v00_26924.map" model { file = "/net/cci-nas-00/data/ceres_data/7v00_26924/06_2025/7v00_26924_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v00_26924/06_2025/7v00_26924_neut.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.35, per 1000 atoms: 0.56 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: 4.49 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 5.69 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: 5.96 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6038 1.33 - 1.46: 4261 1.46 - 1.58: 10386 1.58 - 1.70: 70 1.70 - 1.82: 99 Bond restraints: 20854 Sorted by residual: bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.475 1.386 0.089 1.50e-02 4.44e+03 3.50e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.480 1.567 -0.087 1.50e-02 4.44e+03 3.33e+01 bond pdb=" C1' C G 28 " pdb=" N1 C G 28 " ideal model delta sigma weight residual 1.480 1.565 -0.085 1.50e-02 4.44e+03 3.19e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.475 1.402 0.073 1.50e-02 4.44e+03 2.38e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.470 1.540 -0.070 1.50e-02 4.44e+03 2.16e+01 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27271 2.13 - 4.27: 758 4.27 - 6.40: 128 6.40 - 8.53: 20 8.53 - 10.66: 4 Bond angle restraints: 28181 Sorted by residual: angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 130.39 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 107.01 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" C THR F 539 " pdb=" N PHE F 540 " pdb=" CA PHE F 540 " ideal model delta sigma weight residual 120.31 111.85 8.46 1.52e+00 4.33e-01 3.10e+01 angle pdb=" C5' ATP F 801 " pdb=" O5' ATP F 801 " pdb=" PA ATP F 801 " ideal model delta sigma weight residual 121.27 116.99 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N MET E 186 " pdb=" CA MET E 186 " pdb=" C MET E 186 " ideal model delta sigma weight residual 110.07 104.81 5.26 1.26e+00 6.30e-01 1.74e+01 ... (remaining 28176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 12230 31.68 - 63.35: 327 63.35 - 95.03: 42 95.03 - 126.70: 4 126.70 - 158.37: 3 Dihedral angle restraints: 12606 sinusoidal: 5528 harmonic: 7078 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 50.60 149.40 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -158.23 72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 30.37 -158.37 1 1.70e+01 3.46e-03 6.41e+01 ... (remaining 12603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2509 0.066 - 0.132: 516 0.132 - 0.198: 53 0.198 - 0.264: 8 0.264 - 0.330: 3 Chirality restraints: 3089 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE D 46 " pdb=" CA ILE D 46 " pdb=" CG1 ILE D 46 " pdb=" CG2 ILE D 46 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3086 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.08e-02 2.38e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 339 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 129 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C THR F 129 " 0.067 2.00e-02 2.50e+03 pdb=" O THR F 129 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN F 130 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 85 " -0.022 2.00e-02 2.50e+03 2.20e-02 8.49e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.001 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 156 2.57 - 3.15: 17450 3.15 - 3.73: 30144 3.73 - 4.32: 42625 4.32 - 4.90: 69362 Nonbonded interactions: 159737 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.987 3.120 nonbonded pdb=" O TYR H 71 " pdb=" OH TYR H 162 " model vdw 2.035 3.040 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.056 3.040 nonbonded pdb=" NH1 ARG C 129 " pdb=" OD1 ASN D 57 " model vdw 2.057 3.120 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.118 3.040 ... (remaining 159732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'B' and resid 2 through 208) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 139)) selection = chain 'J' selection = (chain 'K' and (resid 17 through 61 or resid 74 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 45.260 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 20855 Z= 0.323 Angle : 0.862 10.663 28183 Z= 0.497 Chirality : 0.053 0.330 3089 Planarity : 0.004 0.065 3493 Dihedral : 14.507 158.375 8053 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (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 TRP 0.079 0.004 TRP F 339 HIS 0.007 0.002 HIS I 18 PHE 0.051 0.003 PHE I 85 TYR 0.030 0.002 TYR F 582 ARG 0.019 0.002 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.18188 ( 935) hydrogen bonds : angle 7.14156 ( 2712) SS BOND : bond 0.00118 ( 1) SS BOND : angle 1.35683 ( 2) covalent geometry : bond 0.00589 (20854) covalent geometry : angle 0.86219 (28181) *********************** 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 : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 110 HIS cc_start: 0.8270 (t-90) cc_final: 0.7697 (t-170) REVERT: D 131 THR cc_start: 0.8024 (p) cc_final: 0.7390 (p) REVERT: E 28 ASP cc_start: 0.8385 (m-30) cc_final: 0.7785 (m-30) REVERT: E 33 PHE cc_start: 0.8218 (m-10) cc_final: 0.7706 (m-80) REVERT: E 41 ILE cc_start: 0.8233 (mm) cc_final: 0.8017 (mp) REVERT: F 222 ASP cc_start: 0.8014 (m-30) cc_final: 0.7805 (m-30) REVERT: F 624 MET cc_start: 0.7867 (ttm) cc_final: 0.7514 (tpt) REVERT: I 85 PHE cc_start: 0.8837 (m-80) cc_final: 0.8540 (m-80) REVERT: I 104 MET cc_start: 0.8553 (mmm) cc_final: 0.8349 (tmm) REVERT: I 119 PHE cc_start: 0.9040 (t80) cc_final: 0.8747 (t80) REVERT: J 18 HIS cc_start: 0.7377 (t-170) cc_final: 0.6669 (t70) REVERT: J 126 TYR cc_start: 0.8998 (t80) cc_final: 0.8745 (t80) REVERT: K 50 ASN cc_start: 0.8962 (m-40) cc_final: 0.8045 (m110) outliers start: 7 outliers final: 0 residues processed: 449 average time/residue: 0.4024 time to fit residues: 259.5212 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 : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 0.0470 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 168 ASN D 174 HIS D 178 ASN E 60 GLN E 316 ASN E 324 GLN F 14 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 155 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 482 ASN F 560 GLN F 670 ASN F 708 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.061107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.046903 restraints weight = 143208.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048202 restraints weight = 83707.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049049 restraints weight = 56403.965| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3103 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 : 0.728 9.897 28183 Z= 0.388 Chirality : 0.046 0.268 3089 Planarity : 0.004 0.041 3493 Dihedral : 13.853 162.118 3140 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.29 % Allowed : 9.73 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2378 helix: 0.54 (0.16), residues: 1074 sheet: 0.38 (0.26), residues: 390 loop : -1.57 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 339 HIS 0.011 0.001 HIS K 18 PHE 0.032 0.002 PHE K 85 TYR 0.031 0.002 TYR J 86 ARG 0.011 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.05025 ( 935) hydrogen bonds : angle 5.43031 ( 2712) SS BOND : bond 0.00323 ( 1) SS BOND : angle 1.08166 ( 2) covalent geometry : bond 0.00374 (20854) covalent geometry : angle 0.72835 (28181) *********************** 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 256 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 2.251 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 161 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8820 (mp10) REVERT: E 28 ASP cc_start: 0.8802 (m-30) cc_final: 0.8450 (t0) REVERT: E 186 MET cc_start: 0.8709 (mmm) cc_final: 0.8048 (mpp) REVERT: E 259 PHE cc_start: 0.7906 (m-10) cc_final: 0.7468 (m-10) REVERT: F 184 TRP cc_start: 0.5637 (m100) cc_final: 0.4967 (m100) REVERT: F 222 ASP cc_start: 0.8981 (m-30) cc_final: 0.8678 (m-30) REVERT: F 452 MET cc_start: 0.8296 (mmp) cc_final: 0.7504 (mmm) REVERT: F 624 MET cc_start: 0.8491 (ttm) cc_final: 0.7877 (tpp) REVERT: F 695 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.5319 (m-80) REVERT: H 187 LEU cc_start: 0.9097 (mt) cc_final: 0.8856 (mm) REVERT: I 71 ASN cc_start: 0.8584 (p0) cc_final: 0.8103 (p0) REVERT: I 85 PHE cc_start: 0.9122 (m-80) cc_final: 0.8717 (m-80) REVERT: I 86 TYR cc_start: 0.9018 (m-80) cc_final: 0.8316 (m-80) REVERT: I 104 MET cc_start: 0.8774 (mmm) cc_final: 0.8332 (tpp) REVERT: I 127 PHE cc_start: 0.9629 (t80) cc_final: 0.9411 (t80) REVERT: J 18 HIS cc_start: 0.6959 (t-170) cc_final: 0.6483 (t70) REVERT: J 102 THR cc_start: 0.5056 (t) cc_final: 0.4446 (t) REVERT: J 137 TYR cc_start: 0.6932 (m-10) cc_final: 0.6508 (m-80) REVERT: K 85 PHE cc_start: 0.9312 (m-80) cc_final: 0.8926 (m-80) REVERT: K 99 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9207 (mt) REVERT: K 133 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8586 (m-10) outliers start: 28 outliers final: 17 residues processed: 248 average time/residue: 0.3476 time to fit residues: 128.8859 Evaluate side-chains 212 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 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 J residue 45 THR Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 156 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 240 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 40 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN D 110 HIS D 178 ASN E 320 HIS F 38 HIS F 169 HIS ** F 306 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.059232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.045302 restraints weight = 144887.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.046512 restraints weight = 86484.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.047284 restraints weight = 59749.156| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20855 Z= 0.201 Angle : 0.671 9.783 28183 Z= 0.356 Chirality : 0.044 0.416 3089 Planarity : 0.004 0.041 3493 Dihedral : 13.721 165.100 3140 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.89 % Allowed : 10.15 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2378 helix: 0.66 (0.15), residues: 1083 sheet: 0.43 (0.27), residues: 390 loop : -1.54 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 339 HIS 0.010 0.001 HIS K 18 PHE 0.054 0.002 PHE J 85 TYR 0.024 0.002 TYR I 126 ARG 0.007 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 935) hydrogen bonds : angle 5.07299 ( 2712) SS BOND : bond 0.00677 ( 1) SS BOND : angle 0.99072 ( 2) covalent geometry : bond 0.00419 (20854) covalent geometry : angle 0.67071 (28181) *********************** 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 239 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 2.532 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 28 ASP cc_start: 0.8943 (m-30) cc_final: 0.8742 (t0) REVERT: E 97 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6460 (tt0) REVERT: E 186 MET cc_start: 0.8917 (mmm) cc_final: 0.8312 (mpp) REVERT: E 259 PHE cc_start: 0.8928 (m-10) cc_final: 0.8664 (m-80) REVERT: E 327 MET cc_start: 0.9553 (OUTLIER) cc_final: 0.9333 (pmm) REVERT: F 184 TRP cc_start: 0.5592 (m100) cc_final: 0.5170 (m100) REVERT: F 222 ASP cc_start: 0.9007 (m-30) cc_final: 0.8745 (m-30) REVERT: F 452 MET cc_start: 0.8600 (mmp) cc_final: 0.7662 (mmm) REVERT: F 624 MET cc_start: 0.8440 (ttm) cc_final: 0.7940 (tpt) REVERT: F 665 ASP cc_start: 0.9321 (p0) cc_final: 0.9099 (p0) REVERT: F 695 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.4881 (m-80) REVERT: H 13 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8867 (ptpp) REVERT: H 187 LEU cc_start: 0.9229 (mt) cc_final: 0.9027 (mm) REVERT: I 54 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8927 (mm-40) REVERT: I 85 PHE cc_start: 0.9180 (m-80) cc_final: 0.8673 (m-80) REVERT: I 104 MET cc_start: 0.8808 (mmm) cc_final: 0.8455 (tpp) REVERT: I 127 PHE cc_start: 0.9621 (t80) cc_final: 0.9408 (t80) REVERT: J 136 TYR cc_start: 0.5619 (t80) cc_final: 0.5245 (t80) REVERT: J 137 TYR cc_start: 0.6820 (m-10) cc_final: 0.6165 (m-80) REVERT: K 14 MET cc_start: 0.1288 (mtm) cc_final: 0.0963 (mtm) REVERT: K 85 PHE cc_start: 0.9345 (m-80) cc_final: 0.9137 (m-80) REVERT: K 123 TYR cc_start: 0.9545 (t80) cc_final: 0.9283 (t80) REVERT: K 133 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8561 (m-10) outliers start: 41 outliers final: 21 residues processed: 228 average time/residue: 0.3547 time to fit residues: 123.2048 Evaluate side-chains 204 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 318 SER 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 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 109 ASP Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 74 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 122 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS F 43 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.058899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044890 restraints weight = 146501.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046071 restraints weight = 87100.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046838 restraints weight = 60438.407| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20855 Z= 0.173 Angle : 0.619 8.956 28183 Z= 0.329 Chirality : 0.043 0.207 3089 Planarity : 0.003 0.045 3493 Dihedral : 13.612 166.952 3140 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.20 % Allowed : 12.18 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2378 helix: 0.84 (0.16), residues: 1068 sheet: 0.46 (0.26), residues: 400 loop : -1.51 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 339 HIS 0.015 0.001 HIS K 18 PHE 0.049 0.002 PHE J 85 TYR 0.030 0.002 TYR J 126 ARG 0.007 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 935) hydrogen bonds : angle 4.86558 ( 2712) SS BOND : bond 0.00546 ( 1) SS BOND : angle 0.87316 ( 2) covalent geometry : bond 0.00360 (20854) covalent geometry : angle 0.61914 (28181) *********************** 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 214 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 259 PHE cc_start: 0.8773 (m-10) cc_final: 0.8523 (m-80) REVERT: F 184 TRP cc_start: 0.5702 (m100) cc_final: 0.5234 (m100) REVERT: F 222 ASP cc_start: 0.9011 (m-30) cc_final: 0.8749 (m-30) REVERT: F 452 MET cc_start: 0.8709 (mmp) cc_final: 0.7777 (mmm) REVERT: F 624 MET cc_start: 0.8453 (ttm) cc_final: 0.7949 (tpp) REVERT: F 665 ASP cc_start: 0.9250 (p0) cc_final: 0.9001 (p0) REVERT: F 695 TYR cc_start: 0.5661 (OUTLIER) cc_final: 0.5067 (m-80) REVERT: H 13 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8893 (ptpp) REVERT: I 85 PHE cc_start: 0.9149 (m-80) cc_final: 0.8661 (m-80) REVERT: I 96 ASP cc_start: 0.8091 (t0) cc_final: 0.7819 (m-30) REVERT: I 104 MET cc_start: 0.8878 (mmm) cc_final: 0.8501 (tpp) REVERT: I 127 PHE cc_start: 0.9629 (t80) cc_final: 0.9408 (t80) REVERT: J 133 TYR cc_start: 0.7972 (m-80) cc_final: 0.7403 (t80) REVERT: K 85 PHE cc_start: 0.9418 (m-80) cc_final: 0.8999 (m-80) REVERT: K 133 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8583 (m-10) outliers start: 26 outliers final: 14 residues processed: 206 average time/residue: 0.3255 time to fit residues: 102.9704 Evaluate side-chains 190 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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 110 HIS 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 432 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 186 optimal weight: 0.0060 chunk 19 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN D 110 HIS D 155 ASN E 324 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.057569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043772 restraints weight = 147033.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044967 restraints weight = 87153.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045708 restraints weight = 59841.009| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20855 Z= 0.212 Angle : 0.638 9.742 28183 Z= 0.338 Chirality : 0.043 0.208 3089 Planarity : 0.003 0.042 3493 Dihedral : 13.552 169.740 3140 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.85 % Allowed : 12.18 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2378 helix: 0.93 (0.16), residues: 1061 sheet: 0.39 (0.27), residues: 405 loop : -1.52 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.027 0.002 HIS D 110 PHE 0.019 0.002 PHE K 98 TYR 0.025 0.002 TYR K 80 ARG 0.006 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 935) hydrogen bonds : angle 4.80236 ( 2712) SS BOND : bond 0.00691 ( 1) SS BOND : angle 0.78215 ( 2) covalent geometry : bond 0.00439 (20854) covalent geometry : angle 0.63805 (28181) *********************** 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 222 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 2.286 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: E 324 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7290 (pp30) REVERT: F 184 TRP cc_start: 0.5883 (m100) cc_final: 0.5429 (m100) REVERT: F 222 ASP cc_start: 0.8980 (m-30) cc_final: 0.8739 (m-30) REVERT: F 452 MET cc_start: 0.8768 (mmp) cc_final: 0.7792 (mmm) REVERT: F 477 ARG cc_start: 0.9140 (mmt-90) cc_final: 0.8779 (mmp80) REVERT: F 624 MET cc_start: 0.8360 (ttm) cc_final: 0.7945 (tpp) REVERT: F 665 ASP cc_start: 0.9186 (p0) cc_final: 0.8940 (p0) REVERT: F 695 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4848 (m-80) REVERT: H 13 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8981 (ptpp) REVERT: I 85 PHE cc_start: 0.9183 (m-80) cc_final: 0.8720 (m-80) REVERT: J 136 TYR cc_start: 0.5889 (t80) cc_final: 0.5589 (t80) REVERT: J 137 TYR cc_start: 0.7062 (m-10) cc_final: 0.6611 (m-80) REVERT: K 124 CYS cc_start: 0.9750 (OUTLIER) cc_final: 0.9383 (m) REVERT: K 133 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8546 (m-10) outliers start: 40 outliers final: 27 residues processed: 214 average time/residue: 0.3328 time to fit residues: 110.8346 Evaluate side-chains 202 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 2.386 ------------------------------------------------------------------------------- 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 110 HIS 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 322 SER Chi-restraints excluded: chain E residue 324 GLN Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 124 CYS 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 82 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 203 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** 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 = 0.3430 r_free = 0.3430 target = 0.057891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043760 restraints weight = 144404.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.044986 restraints weight = 85246.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045795 restraints weight = 58313.712| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20855 Z= 0.152 Angle : 0.608 10.711 28183 Z= 0.319 Chirality : 0.042 0.343 3089 Planarity : 0.003 0.036 3493 Dihedral : 13.432 170.244 3140 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.94 % Allowed : 12.92 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2378 helix: 1.01 (0.16), residues: 1069 sheet: 0.38 (0.26), residues: 409 loop : -1.46 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 594 HIS 0.014 0.001 HIS D 110 PHE 0.025 0.002 PHE J 85 TYR 0.028 0.001 TYR J 126 ARG 0.007 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 935) hydrogen bonds : angle 4.67614 ( 2712) SS BOND : bond 0.00409 ( 1) SS BOND : angle 0.77567 ( 2) covalent geometry : bond 0.00322 (20854) covalent geometry : angle 0.60752 (28181) *********************** 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 220 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 2.374 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: 0.9708 (OUTLIER) cc_final: 0.9424 (ttpp) REVERT: C 88 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8134 (mttt) REVERT: E 259 PHE cc_start: 0.8127 (m-10) cc_final: 0.7744 (m-80) REVERT: E 327 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9290 (mtm) REVERT: F 1 MET cc_start: 0.8302 (mmt) cc_final: 0.7508 (tpp) REVERT: F 184 TRP cc_start: 0.6055 (m100) cc_final: 0.5575 (m100) REVERT: F 222 ASP cc_start: 0.9045 (m-30) cc_final: 0.8791 (m-30) REVERT: F 452 MET cc_start: 0.8802 (mmp) cc_final: 0.7736 (mmm) REVERT: F 507 ASP cc_start: 0.5571 (OUTLIER) cc_final: 0.5173 (p0) REVERT: F 624 MET cc_start: 0.8364 (ttm) cc_final: 0.7951 (tpp) REVERT: F 665 ASP cc_start: 0.9210 (p0) cc_final: 0.8971 (p0) REVERT: F 695 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.4833 (m-80) REVERT: H 13 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9009 (ptpp) REVERT: I 85 PHE cc_start: 0.9111 (m-80) cc_final: 0.8689 (m-80) REVERT: I 96 ASP cc_start: 0.7848 (t0) cc_final: 0.7542 (m-30) REVERT: J 133 TYR cc_start: 0.8001 (m-80) cc_final: 0.7507 (t80) REVERT: K 133 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8580 (m-10) outliers start: 42 outliers final: 24 residues processed: 211 average time/residue: 0.3384 time to fit residues: 109.0251 Evaluate side-chains 198 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 2.410 ------------------------------------------------------------------------------- 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 88 LYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 507 ASP Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 229 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 141 optimal weight: 0.0870 chunk 150 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.058347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.044494 restraints weight = 145179.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045727 restraints weight = 85730.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046549 restraints weight = 58426.780| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20855 Z= 0.120 Angle : 0.606 9.577 28183 Z= 0.318 Chirality : 0.043 0.271 3089 Planarity : 0.003 0.036 3493 Dihedral : 13.267 170.717 3140 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.38 % Allowed : 14.07 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2378 helix: 1.16 (0.16), residues: 1058 sheet: 0.43 (0.26), residues: 415 loop : -1.35 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 339 HIS 0.023 0.001 HIS D 110 PHE 0.044 0.001 PHE J 85 TYR 0.026 0.001 TYR K 80 ARG 0.007 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 935) hydrogen bonds : angle 4.54166 ( 2712) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.84086 ( 2) covalent geometry : bond 0.00250 (20854) covalent geometry : angle 0.60597 (28181) *********************** 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 206 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 2.500 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: 0.9706 (OUTLIER) cc_final: 0.9460 (ttpp) REVERT: C 55 MET cc_start: 0.9704 (mtp) cc_final: 0.9339 (mpp) REVERT: E 259 PHE cc_start: 0.7940 (m-10) cc_final: 0.7580 (m-80) REVERT: F 1 MET cc_start: 0.8312 (mmt) cc_final: 0.7503 (tpp) REVERT: F 184 TRP cc_start: 0.6015 (m100) cc_final: 0.5557 (m100) REVERT: F 222 ASP cc_start: 0.8986 (m-30) cc_final: 0.8730 (m-30) REVERT: F 452 MET cc_start: 0.8680 (mmp) cc_final: 0.7679 (mmm) REVERT: F 507 ASP cc_start: 0.5465 (OUTLIER) cc_final: 0.5251 (p0) REVERT: F 624 MET cc_start: 0.8447 (ttm) cc_final: 0.7871 (ttt) REVERT: F 665 ASP cc_start: 0.9218 (p0) cc_final: 0.8981 (p0) REVERT: F 695 TYR cc_start: 0.5264 (OUTLIER) cc_final: 0.4803 (m-80) REVERT: F 721 MET cc_start: 0.6903 (mtt) cc_final: 0.6361 (ttt) REVERT: H 13 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8891 (ptpp) REVERT: I 85 PHE cc_start: 0.9089 (m-80) cc_final: 0.8768 (m-80) REVERT: J 136 TYR cc_start: 0.5998 (t80) cc_final: 0.5717 (t80) REVERT: J 137 TYR cc_start: 0.7177 (m-10) cc_final: 0.6883 (m-80) REVERT: K 85 PHE cc_start: 0.9649 (m-80) cc_final: 0.9437 (m-80) REVERT: K 133 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8572 (m-10) outliers start: 30 outliers final: 20 residues processed: 199 average time/residue: 0.3402 time to fit residues: 103.7086 Evaluate side-chains 189 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 110 HIS Chi-restraints excluded: chain D residue 195 LYS 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 507 ASP Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 83 ILE 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 25 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS D 110 HIS ** 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** K 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.055669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.042026 restraints weight = 153278.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043174 restraints weight = 89619.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043876 restraints weight = 60830.456| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20855 Z= 0.276 Angle : 0.732 12.641 28183 Z= 0.382 Chirality : 0.045 0.213 3089 Planarity : 0.004 0.036 3493 Dihedral : 13.409 173.001 3140 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.71 % Allowed : 14.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2378 helix: 0.83 (0.16), residues: 1064 sheet: 0.32 (0.26), residues: 405 loop : -1.42 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 301 HIS 0.039 0.002 HIS D 110 PHE 0.037 0.002 PHE J 85 TYR 0.030 0.002 TYR J 126 ARG 0.008 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 935) hydrogen bonds : angle 4.83522 ( 2712) SS BOND : bond 0.01013 ( 1) SS BOND : angle 0.88688 ( 2) covalent geometry : bond 0.00573 (20854) covalent geometry : angle 0.73213 (28181) *********************** 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 210 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9717 (OUTLIER) cc_final: 0.9373 (ttpp) REVERT: C 88 LYS cc_start: 0.8545 (mttt) cc_final: 0.8043 (mptt) REVERT: E 186 MET cc_start: 0.8020 (mmm) cc_final: 0.7561 (mpp) REVERT: E 259 PHE cc_start: 0.8276 (m-10) cc_final: 0.7995 (m-80) REVERT: F 184 TRP cc_start: 0.6316 (m100) cc_final: 0.5820 (m100) REVERT: F 358 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8370 (t) REVERT: F 452 MET cc_start: 0.8869 (mmp) cc_final: 0.7876 (mmm) REVERT: F 624 MET cc_start: 0.8371 (ttm) cc_final: 0.8144 (ttt) REVERT: F 665 ASP cc_start: 0.9238 (p0) cc_final: 0.9009 (p0) REVERT: F 695 TYR cc_start: 0.5189 (OUTLIER) cc_final: 0.4602 (m-80) REVERT: F 721 MET cc_start: 0.6898 (mtt) cc_final: 0.6093 (ttt) REVERT: I 37 GLN cc_start: 0.3032 (mt0) cc_final: 0.2423 (tm-30) REVERT: I 85 PHE cc_start: 0.9079 (m-80) cc_final: 0.8656 (m-80) REVERT: J 133 TYR cc_start: 0.8124 (m-80) cc_final: 0.7739 (t80) REVERT: K 50 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (p0) REVERT: K 85 PHE cc_start: 0.9628 (m-80) cc_final: 0.9288 (m-80) REVERT: K 133 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8576 (m-10) outliers start: 37 outliers final: 30 residues processed: 202 average time/residue: 0.3378 time to fit residues: 104.8544 Evaluate side-chains 199 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 318 SER 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 358 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 142 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS D 110 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 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** K 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.057085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.042983 restraints weight = 145801.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044119 restraints weight = 87180.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044842 restraints weight = 60722.726| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20855 Z= 0.133 Angle : 0.639 11.788 28183 Z= 0.332 Chirality : 0.043 0.239 3089 Planarity : 0.003 0.035 3493 Dihedral : 13.278 171.805 3140 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.34 % Allowed : 15.41 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2378 helix: 1.02 (0.16), residues: 1065 sheet: 0.36 (0.26), residues: 411 loop : -1.30 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 594 HIS 0.011 0.001 HIS K 18 PHE 0.048 0.002 PHE J 85 TYR 0.025 0.001 TYR J 126 ARG 0.009 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 935) hydrogen bonds : angle 4.63441 ( 2712) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.88010 ( 2) covalent geometry : bond 0.00281 (20854) covalent geometry : angle 0.63883 (28181) *********************** 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 200 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9712 (OUTLIER) cc_final: 0.9428 (ttpp) REVERT: C 88 LYS cc_start: 0.8502 (mttt) cc_final: 0.8036 (mptt) REVERT: E 181 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (mmmt) REVERT: E 186 MET cc_start: 0.8295 (mmm) cc_final: 0.7829 (mpp) REVERT: E 259 PHE cc_start: 0.8154 (m-10) cc_final: 0.7807 (m-80) REVERT: F 1 MET cc_start: 0.8388 (mmt) cc_final: 0.7544 (tpp) REVERT: F 8 MET cc_start: 0.9302 (mmp) cc_final: 0.8897 (mmp) REVERT: F 184 TRP cc_start: 0.6116 (m100) cc_final: 0.5660 (m100) REVERT: F 222 ASP cc_start: 0.9008 (m-30) cc_final: 0.8758 (m-30) REVERT: F 358 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8380 (t) REVERT: F 452 MET cc_start: 0.8728 (mmp) cc_final: 0.7756 (mmm) REVERT: F 665 ASP cc_start: 0.9207 (p0) cc_final: 0.8941 (p0) REVERT: F 695 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4788 (m-80) REVERT: F 721 MET cc_start: 0.6883 (mtt) cc_final: 0.6209 (ttt) REVERT: I 37 GLN cc_start: 0.2730 (mt0) cc_final: 0.2149 (tm-30) REVERT: I 85 PHE cc_start: 0.9077 (m-80) cc_final: 0.8763 (m-80) REVERT: J 18 HIS cc_start: 0.8262 (t-90) cc_final: 0.7792 (t-90) REVERT: J 136 TYR cc_start: 0.6070 (t80) cc_final: 0.5760 (t80) REVERT: J 137 TYR cc_start: 0.7187 (m-10) cc_final: 0.6802 (m-80) REVERT: K 85 PHE cc_start: 0.9668 (m-80) cc_final: 0.9314 (m-80) REVERT: K 123 TYR cc_start: 0.9404 (t80) cc_final: 0.9047 (t80) REVERT: K 133 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8539 (m-10) outliers start: 29 outliers final: 20 residues processed: 196 average time/residue: 0.3459 time to fit residues: 103.1945 Evaluate side-chains 191 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 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 358 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 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 220 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS ** D 168 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 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042539 restraints weight = 151786.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043680 restraints weight = 88939.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.044374 restraints weight = 60447.230| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20855 Z= 0.211 Angle : 0.678 14.695 28183 Z= 0.354 Chirality : 0.043 0.253 3089 Planarity : 0.003 0.034 3493 Dihedral : 13.297 172.772 3140 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.29 % Allowed : 15.77 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2378 helix: 0.97 (0.16), residues: 1059 sheet: 0.32 (0.26), residues: 403 loop : -1.36 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 594 HIS 0.013 0.001 HIS D 110 PHE 0.036 0.002 PHE I 98 TYR 0.027 0.002 TYR J 126 ARG 0.009 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 935) hydrogen bonds : angle 4.73980 ( 2712) SS BOND : bond 0.00666 ( 1) SS BOND : angle 0.75685 ( 2) covalent geometry : bond 0.00439 (20854) covalent geometry : angle 0.67830 (28181) ********************** 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 199 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.411 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: A 171 LYS cc_start: 0.9718 (OUTLIER) cc_final: 0.9439 (ttpp) REVERT: C 88 LYS cc_start: 0.8492 (mttt) cc_final: 0.8030 (mptt) REVERT: E 181 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8465 (mmmt) REVERT: E 186 MET cc_start: 0.8280 (mmm) cc_final: 0.7808 (mpp) REVERT: E 259 PHE cc_start: 0.8093 (m-10) cc_final: 0.7854 (m-80) REVERT: F 1 MET cc_start: 0.8442 (mmt) cc_final: 0.7580 (tpp) REVERT: F 184 TRP cc_start: 0.6231 (m100) cc_final: 0.5775 (m100) REVERT: F 358 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8320 (t) REVERT: F 452 MET cc_start: 0.8761 (mmp) cc_final: 0.7931 (mmm) REVERT: F 477 ARG cc_start: 0.9184 (mmt-90) cc_final: 0.8813 (mmp80) REVERT: F 496 MET cc_start: 0.7865 (pmm) cc_final: 0.7586 (pmm) REVERT: F 665 ASP cc_start: 0.9250 (p0) cc_final: 0.9015 (p0) REVERT: F 695 TYR cc_start: 0.5146 (OUTLIER) cc_final: 0.4607 (m-80) REVERT: I 85 PHE cc_start: 0.9146 (m-80) cc_final: 0.8692 (m-80) REVERT: J 136 TYR cc_start: 0.6100 (t80) cc_final: 0.5859 (t80) REVERT: J 137 TYR cc_start: 0.7174 (m-10) cc_final: 0.6866 (m-80) REVERT: K 85 PHE cc_start: 0.9620 (m-80) cc_final: 0.9224 (m-80) REVERT: K 123 TYR cc_start: 0.9401 (t80) cc_final: 0.9026 (t80) REVERT: K 133 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8530 (m-10) outliers start: 28 outliers final: 22 residues processed: 195 average time/residue: 0.3547 time to fit residues: 105.7349 Evaluate side-chains 186 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 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 358 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain K residue 133 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 229 optimal weight: 0.0970 chunk 224 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS ** D 168 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.055747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042054 restraints weight = 152071.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043239 restraints weight = 87460.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044021 restraints weight = 59068.169| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20855 Z= 0.212 Angle : 0.683 12.837 28183 Z= 0.357 Chirality : 0.044 0.263 3089 Planarity : 0.003 0.035 3493 Dihedral : 13.330 172.876 3140 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.52 % Allowed : 15.96 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2378 helix: 0.94 (0.16), residues: 1055 sheet: 0.22 (0.26), residues: 405 loop : -1.37 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 495 HIS 0.019 0.002 HIS D 110 PHE 0.029 0.002 PHE E 222 TYR 0.027 0.002 TYR K 80 ARG 0.011 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 935) hydrogen bonds : angle 4.74798 ( 2712) SS BOND : bond 0.00665 ( 1) SS BOND : angle 0.81875 ( 2) covalent geometry : bond 0.00441 (20854) covalent geometry : angle 0.68320 (28181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6736.96 seconds wall clock time: 118 minutes 33.00 seconds (7113.00 seconds total)