Starting phenix.real_space_refine on Sun Sep 13 17:26:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2026/6w6v_21564.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.094 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 295 5.49 5 S 90 5.16 5 C 14572 2.51 5 N 4418 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24850 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 294, 6239 Classifications: {'RNAv2': 294} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 21, 'rna3p_pur': 125, 'rna3p_pyr': 124} Link IDs: {'rna2p': 45, 'rna3p': 248} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 294, 6239 Classifications: {'RNAv2': 294} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 21, 'rna3p_pur': 125, 'rna3p_pyr': 124} Link IDs: {'rna2p': 45, 'rna3p': 248} Chain breaks: 7 bond proxies already assigned to first conformer: 6942 Chain: "B" Number of atoms: 6345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6345 Classifications: {'peptide': 780} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 743} Chain breaks: 3 Chain: "D" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1759 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "E" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1335 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "F" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1280 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "G" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1006 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1033 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain: "I" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1891 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 648 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1032 Classifications: {'peptide': 121} Link IDs: {'TRANS': 120} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A A A 113 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A A 113 " occ=0.50 Time building chain proxies: 5.93, per 1000 atoms: 0.24 Number of scatterers: 24850 At special positions: 0 Unit cell: (125.685, 156.94, 150.29, 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 90 16.00 P 295 15.00 O 5475 8.00 N 4418 7.00 C 14572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 777.6 milliseconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 15 sheets defined 36.9% alpha, 13.9% beta 78 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.954A pdb=" N ALA B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.173A pdb=" N ARG B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 122 removed outlier: 3.686A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.021A pdb=" N LYS B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.567A pdb=" N LYS B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.622A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.866A pdb=" N VAL B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 381 " --> pdb=" O GLN B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.669A pdb=" N LEU B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.823A pdb=" N GLN B 466 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.503A pdb=" N HIS B 479 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 removed outlier: 3.769A pdb=" N VAL B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 520 through 523 removed outlier: 4.090A pdb=" N ALA B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.659A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 573 " --> pdb=" O TRP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.806A pdb=" N ILE B 610 " --> pdb=" O GLN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.933A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 674 removed outlier: 3.898A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 714 Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.562A pdb=" N ILE B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 844 through 848' Processing helix chain 'D' and resid 77 through 105 removed outlier: 3.667A pdb=" N LYS D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU D 91 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 removed outlier: 3.574A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 130 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.037A pdb=" N ILE D 151 " --> pdb=" O TRP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.569A pdb=" N SER D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.672A pdb=" N LEU E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.695A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.692A pdb=" N ASN E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 123 through 142 removed outlier: 3.652A pdb=" N GLU E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 155 through 162 removed outlier: 3.597A pdb=" N PHE E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS E 160 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.735A pdb=" N VAL F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.747A pdb=" N SER F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 102 " --> pdb=" O PHE F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.929A pdb=" N LYS G 74 " --> pdb=" O LYS G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 47 through 51 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.513A pdb=" N SER H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'I' and resid 19 through 37 removed outlier: 4.196A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 142 through 152 removed outlier: 3.776A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 166 removed outlier: 3.851A pdb=" N ARG I 165 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP I 166 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 166' Processing helix chain 'I' and resid 166 through 184 removed outlier: 3.608A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.001A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 239 removed outlier: 3.587A pdb=" N LEU I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 243 removed outlier: 3.700A pdb=" N HIS I 243 " --> pdb=" O ASN I 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 240 through 243' Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.540A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.607A pdb=" N LEU J 60 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.517A pdb=" N PHE J 69 " --> pdb=" O ILE J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 77 Processing helix chain 'J' and resid 99 through 104 removed outlier: 3.589A pdb=" N ALA J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 99 through 104' Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 146 through 151 removed outlier: 4.140A pdb=" N ASN J 151 " --> pdb=" O CYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.827A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 161 through 165' Processing helix chain 'J' and resid 167 through 184 removed outlier: 4.361A pdb=" N ARG J 171 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 Processing helix chain 'J' and resid 203 through 206 Processing helix chain 'J' and resid 207 through 213 removed outlier: 3.770A pdb=" N ASN J 213 " --> pdb=" O SER J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 225 removed outlier: 4.172A pdb=" N MET J 225 " --> pdb=" O CYS J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'K' and resid 8 through 23 removed outlier: 4.173A pdb=" N ARG K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 46 Processing helix chain 'L' and resid 7 through 25 removed outlier: 4.378A pdb=" N GLN L 13 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.862A pdb=" N ARG L 30 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 50 removed outlier: 4.921A pdb=" N GLU L 40 " --> pdb=" O GLY L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 76 removed outlier: 3.824A pdb=" N ARG L 72 " --> pdb=" O LYS L 69 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG L 76 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 89 Processing helix chain 'L' and resid 90 through 96 removed outlier: 3.661A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 122 removed outlier: 4.048A pdb=" N ILE L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 251 through 252 removed outlier: 6.964A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 446 through 450 removed outlier: 6.334A pdb=" N ALA B 285 " --> pdb=" O TYR B 579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 338 removed outlier: 3.519A pdb=" N PHE B 334 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 358 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 336 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 356 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 354 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 297 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 769 removed outlier: 5.478A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 841 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE B 824 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 843 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 822 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 820 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 783 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 219 through 223 removed outlier: 7.295A pdb=" N ILE D 209 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 219 through 223 removed outlier: 7.295A pdb=" N ILE D 209 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 73 through 77 removed outlier: 6.034A pdb=" N LEU E 74 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG E 87 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR E 76 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 48 removed outlier: 6.947A pdb=" N HIS F 47 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N TYR F 84 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.967A pdb=" N THR G 16 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU G 102 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 55 through 57 removed outlier: 3.922A pdb=" N ILE H 67 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.471A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 156 through 158 removed outlier: 6.267A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 3 through 4 removed outlier: 7.193A pdb=" N ASP J 4 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.864A pdb=" N LEU J 128 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU J 157 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 366 hydrogen bond angles 0 basepair planarities 78 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.80 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: 5800 1.33 - 1.45: 6533 1.45 - 1.57: 12859 1.57 - 1.69: 584 1.69 - 1.81: 139 Bond restraints: 25915 Sorted by residual: bond pdb=" C PRO B 171 " pdb=" N PRO B 172 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.07e+00 bond pdb=" CB PRO I 54 " pdb=" CG PRO I 54 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.84e+00 bond pdb=" CG1 ILE J 181 " pdb=" CD1 ILE J 181 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.33e+00 bond pdb=" CG PRO I 54 " pdb=" CD PRO I 54 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.22e+00 bond pdb=" CG LEU G 66 " pdb=" CD2 LEU G 66 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 ... (remaining 25910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 35586 2.68 - 5.36: 746 5.36 - 8.04: 22 8.04 - 10.72: 6 10.72 - 13.40: 1 Bond angle restraints: 36361 Sorted by residual: angle pdb=" C TYR K 68 " pdb=" N VAL K 69 " pdb=" CA VAL K 69 " ideal model delta sigma weight residual 123.25 117.24 6.01 1.10e+00 8.26e-01 2.99e+01 angle pdb=" CA ARG B 626 " pdb=" CB ARG B 626 " pdb=" CG ARG B 626 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CA LEU G 66 " pdb=" CB LEU G 66 " pdb=" CG LEU G 66 " ideal model delta sigma weight residual 116.30 129.70 -13.40 3.50e+00 8.16e-02 1.47e+01 angle pdb=" CA PRO I 54 " pdb=" N PRO I 54 " pdb=" CD PRO I 54 " ideal model delta sigma weight residual 112.00 106.75 5.25 1.40e+00 5.10e-01 1.41e+01 angle pdb=" CA GLY I 192 " pdb=" C GLY I 192 " pdb=" N SER I 193 " ideal model delta sigma weight residual 114.65 117.93 -3.28 9.20e-01 1.18e+00 1.27e+01 ... (remaining 36356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 12915 17.43 - 34.86: 1499 34.86 - 52.30: 440 52.30 - 69.73: 235 69.73 - 87.16: 53 Dihedral angle restraints: 15142 sinusoidal: 8381 harmonic: 6761 Sorted by residual: dihedral pdb=" C4' A A 261 " pdb=" C3' A A 261 " pdb=" C2' A A 261 " pdb=" C1' A A 261 " ideal model delta sinusoidal sigma weight residual 36.34 -37.65 74.00 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' G A 83 " pdb=" C3' G A 83 " pdb=" C2' G A 83 " pdb=" C1' G A 83 " ideal model delta sinusoidal sigma weight residual 36.35 -37.59 73.93 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' U A 218 " pdb=" C3' U A 218 " pdb=" C2' U A 218 " pdb=" C1' U A 218 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.69 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 15139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3403 0.061 - 0.122: 506 0.122 - 0.183: 47 0.183 - 0.244: 288 0.244 - 0.305: 101 Chirality restraints: 4345 Sorted by residual: chirality pdb=" P U A 124 " pdb=" OP1 U A 124 " pdb=" OP2 U A 124 " pdb=" O5' U A 124 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C3' G A 83 " pdb=" C4' G A 83 " pdb=" O3' G A 83 " pdb=" C2' G A 83 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2' G A 79 " pdb=" C3' G A 79 " pdb=" O2' G A 79 " pdb=" C1' G A 79 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 4342 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE I 53 " -0.066 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO I 54 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO I 54 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO I 54 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 140 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO D 141 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 561 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.031 5.00e-02 4.00e+02 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 549 2.65 - 3.22: 21917 3.22 - 3.78: 36703 3.78 - 4.34: 50494 4.34 - 4.90: 78226 Nonbonded interactions: 187889 Sorted by model distance: nonbonded pdb=" OG SER K 33 " pdb=" O VAL K 69 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR B 242 " pdb=" OD2 ASP B 289 " model vdw 2.104 3.040 nonbonded pdb=" O ASP H 75 " pdb=" OG SER H 79 " model vdw 2.145 3.040 nonbonded pdb=" O GLY I 206 " pdb=" OG SER I 209 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU H 54 " pdb=" OG SER I 179 " model vdw 2.204 3.040 ... (remaining 187884 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.600 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: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.004 0.084 25915 Z= 0.184 Angle : 0.794 13.397 36361 Z= 0.387 Chirality : 0.082 0.305 4345 Planarity : 0.004 0.097 3525 Dihedral : 17.282 87.159 10752 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.17), residues: 2276 helix: -0.56 (0.20), residues: 725 sheet: -0.45 (0.28), residues: 356 loop : -2.79 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 626 TYR 0.032 0.002 TYR L 35 PHE 0.025 0.001 PHE G 51 TRP 0.010 0.001 TRP B 870 HIS 0.007 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (25915) covalent geometry : angle 0.79384 / 0.39 (36361) hydrogen bonds : bond 0.15780 / 8.15 ( 792) hydrogen bonds : angle 6.08986 / 2.48 ( 2067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 ARG cc_start: 0.7695 (tmt170) cc_final: 0.6940 (tmt170) REVERT: B 811 LYS cc_start: 0.7745 (mmpt) cc_final: 0.7537 (ptmt) REVERT: B 849 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7840 (ptt90) REVERT: E 76 TYR cc_start: 0.8412 (t80) cc_final: 0.8147 (t80) REVERT: G 104 ILE cc_start: 0.8412 (pt) cc_final: 0.8073 (pp) REVERT: I 125 ASP cc_start: 0.7921 (m-30) cc_final: 0.7209 (t0) REVERT: J 72 LEU cc_start: 0.8302 (tt) cc_final: 0.8094 (mp) REVERT: J 123 ASN cc_start: 0.7096 (t0) cc_final: 0.6872 (t0) REVERT: K 8 LYS cc_start: 0.8539 (tmmt) cc_final: 0.8325 (ttmt) outliers start: 1 outliers final: 1 residues processed: 384 average time/residue: 0.6577 time to fit residues: 291.2562 Evaluate side-chains 272 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 18 HIS H 36 GLN H 71 HIS J 168 GLN J 240 ASN J 264 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101973 restraints weight = 70882.013| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.64 r_work: 0.3209 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 25915 Z= 0.239 Angle : 1.051 19.110 36361 Z= 0.451 Chirality : 0.090 1.084 4345 Planarity : 0.005 0.067 3525 Dihedral : 15.591 160.440 6040 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 2.67 % Allowed : 13.41 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.17), residues: 2276 helix: -0.25 (0.20), residues: 735 sheet: -0.37 (0.28), residues: 350 loop : -2.82 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 122 TYR 0.025 0.002 TYR I 160 PHE 0.020 0.002 PHE K 72 TRP 0.023 0.002 TRP L 87 HIS 0.006 0.001 HIS I 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (25915) covalent geometry : angle 1.05140 / 0.45 (36361) hydrogen bonds : bond 0.05547 / 2.85 ( 792) hydrogen bonds : angle 4.68083 / 1.92 ( 2067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 811 LYS cc_start: 0.8050 (mmpt) cc_final: 0.7352 (ptmt) REVERT: B 843 ASP cc_start: 0.8837 (t70) cc_final: 0.8422 (t70) REVERT: B 849 ARG cc_start: 0.8563 (mtm110) cc_final: 0.7889 (ptt90) REVERT: D 91 GLU cc_start: 0.7739 (pp20) cc_final: 0.7274 (tm-30) REVERT: D 268 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7907 (mtp85) REVERT: F 49 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (mm) REVERT: F 122 ARG cc_start: 0.8655 (mtm110) cc_final: 0.8424 (mtm110) REVERT: F 130 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: F 132 ARG cc_start: 0.7345 (pmm-80) cc_final: 0.6835 (pmt170) REVERT: G 70 LYS cc_start: 0.7999 (mmpt) cc_final: 0.7793 (tptm) REVERT: G 102 GLU cc_start: 0.7757 (mp0) cc_final: 0.7450 (mp0) REVERT: G 104 ILE cc_start: 0.8293 (pt) cc_final: 0.7944 (pp) REVERT: H 13 LYS cc_start: 0.7218 (tttt) cc_final: 0.6986 (ttpt) REVERT: H 118 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.7969 (m-90) REVERT: I 125 ASP cc_start: 0.8091 (m-30) cc_final: 0.7160 (t0) REVERT: I 136 ARG cc_start: 0.8072 (tpm170) cc_final: 0.7006 (tpt90) REVERT: J 123 ASN cc_start: 0.6998 (t0) cc_final: 0.6737 (t0) REVERT: K 8 LYS cc_start: 0.8405 (tmmt) cc_final: 0.8134 (ttmt) outliers start: 56 outliers final: 17 residues processed: 315 average time/residue: 0.6735 time to fit residues: 244.3825 Evaluate side-chains 280 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 147 CYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 132 optimal weight: 0.0970 chunk 180 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 GLN L 75 GLN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106332 restraints weight = 92279.743| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.21 r_work: 0.3268 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25915 Z= 0.126 Angle : 0.827 13.718 36361 Z= 0.361 Chirality : 0.067 0.602 4345 Planarity : 0.004 0.060 3525 Dihedral : 15.145 169.010 6038 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.24 % Allowed : 16.13 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2276 helix: 0.23 (0.21), residues: 729 sheet: -0.04 (0.29), residues: 343 loop : -2.65 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 550 TYR 0.025 0.001 TYR K 37 PHE 0.022 0.001 PHE K 72 TRP 0.010 0.001 TRP B 624 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (25915) covalent geometry : angle 0.82731 / 0.36 (36361) hydrogen bonds : bond 0.03947 / 2.04 ( 792) hydrogen bonds : angle 4.21063 / 1.74 ( 2067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8308 (tp30) cc_final: 0.8086 (tp30) REVERT: B 393 ASP cc_start: 0.8199 (m-30) cc_final: 0.7590 (t70) REVERT: B 486 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7818 (mt-10) REVERT: B 626 ARG cc_start: 0.8697 (ttt-90) cc_final: 0.8261 (ttt-90) REVERT: B 811 LYS cc_start: 0.8082 (mmpt) cc_final: 0.7381 (ptmt) REVERT: B 843 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8426 (t0) REVERT: D 91 GLU cc_start: 0.7729 (pp20) cc_final: 0.7515 (mm-30) REVERT: D 142 MET cc_start: 0.7907 (ptt) cc_final: 0.7545 (ptp) REVERT: D 268 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8071 (mtp85) REVERT: F 49 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8582 (mm) REVERT: F 122 ARG cc_start: 0.8590 (mtm110) cc_final: 0.8331 (mtm110) REVERT: F 132 ARG cc_start: 0.7396 (pmm-80) cc_final: 0.6687 (pmt170) REVERT: G 70 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7807 (tppp) REVERT: G 98 GLU cc_start: 0.8479 (pm20) cc_final: 0.7996 (mt-10) REVERT: H 13 LYS cc_start: 0.7099 (tttt) cc_final: 0.6850 (ttpt) REVERT: H 118 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.8029 (m-90) REVERT: I 125 ASP cc_start: 0.8114 (m-30) cc_final: 0.7159 (t0) REVERT: J 123 ASN cc_start: 0.7042 (t0) cc_final: 0.6772 (t0) REVERT: K 8 LYS cc_start: 0.8320 (tmmt) cc_final: 0.8073 (ttmt) outliers start: 47 outliers final: 18 residues processed: 341 average time/residue: 0.6060 time to fit residues: 240.7010 Evaluate side-chains 287 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 42 ASN Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN I 102 GLN J 283 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099643 restraints weight = 81443.674| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.88 r_work: 0.3157 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 25915 Z= 0.272 Angle : 0.981 14.024 36361 Z= 0.433 Chirality : 0.079 0.882 4345 Planarity : 0.005 0.069 3525 Dihedral : 15.207 169.324 6038 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 3.39 % Allowed : 19.43 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.17), residues: 2276 helix: -0.12 (0.20), residues: 742 sheet: -0.27 (0.28), residues: 354 loop : -2.75 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 849 TYR 0.027 0.002 TYR H 84 PHE 0.014 0.002 PHE D 208 TRP 0.014 0.002 TRP L 120 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.27 (25915) covalent geometry : angle 0.98085 / 0.43 (36361) hydrogen bonds : bond 0.05936 / 3.03 ( 792) hydrogen bonds : angle 4.48195 / 1.84 ( 2067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: B 291 SER cc_start: 0.8959 (m) cc_final: 0.8759 (m) REVERT: B 393 ASP cc_start: 0.8225 (m-30) cc_final: 0.7728 (t70) REVERT: B 486 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8039 (mt-10) REVERT: B 584 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8443 (ttp-170) REVERT: B 626 ARG cc_start: 0.8766 (ttt-90) cc_final: 0.8205 (ttt-90) REVERT: B 811 LYS cc_start: 0.8072 (mmpt) cc_final: 0.7275 (ptmt) REVERT: B 843 ASP cc_start: 0.8851 (t70) cc_final: 0.8492 (t0) REVERT: D 142 MET cc_start: 0.8029 (ptt) cc_final: 0.7653 (ptp) REVERT: D 268 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (mtp85) REVERT: F 49 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8606 (mm) REVERT: F 130 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: F 132 ARG cc_start: 0.7609 (pmm-80) cc_final: 0.6860 (pmt170) REVERT: G 52 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8655 (mp) REVERT: G 102 GLU cc_start: 0.7956 (mp0) cc_final: 0.7444 (mp0) REVERT: G 104 ILE cc_start: 0.8269 (pt) cc_final: 0.7953 (pp) REVERT: H 7 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7999 (mtt90) REVERT: H 118 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7998 (m-90) REVERT: I 136 ARG cc_start: 0.8277 (tpm170) cc_final: 0.7157 (tpt90) REVERT: J 123 ASN cc_start: 0.7253 (t0) cc_final: 0.6912 (t0) REVERT: J 136 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7672 (mtm180) REVERT: K 8 LYS cc_start: 0.8347 (tmmt) cc_final: 0.8120 (ttmt) outliers start: 71 outliers final: 32 residues processed: 314 average time/residue: 0.6011 time to fit residues: 221.0147 Evaluate side-chains 287 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 221 CYS Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 117 MET Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 176 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 0.1980 chunk 135 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 612 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 GLN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105471 restraints weight = 68075.420| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.60 r_work: 0.3263 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25915 Z= 0.133 Angle : 0.823 11.472 36361 Z= 0.362 Chirality : 0.065 0.537 4345 Planarity : 0.004 0.062 3525 Dihedral : 15.113 172.037 6038 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.15 % Allowed : 20.29 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 2276 helix: 0.27 (0.21), residues: 738 sheet: -0.07 (0.28), residues: 350 loop : -2.60 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 122 TYR 0.026 0.001 TYR J 160 PHE 0.017 0.001 PHE K 72 TRP 0.010 0.001 TRP B 556 HIS 0.008 0.001 HIS L 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25915) covalent geometry : angle 0.82256 / 0.36 (36361) hydrogen bonds : bond 0.04084 / 2.09 ( 792) hydrogen bonds : angle 4.13106 / 1.71 ( 2067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7987 (pp) REVERT: B 119 GLU cc_start: 0.8467 (tp30) cc_final: 0.8189 (tp30) REVERT: B 393 ASP cc_start: 0.8243 (m-30) cc_final: 0.7753 (t70) REVERT: B 486 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7903 (mt-10) REVERT: B 626 ARG cc_start: 0.8773 (ttt-90) cc_final: 0.8196 (ttt-90) REVERT: B 684 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6906 (mtt) REVERT: B 811 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7301 (ptmt) REVERT: B 843 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8404 (t0) REVERT: D 142 MET cc_start: 0.7901 (ptt) cc_final: 0.7519 (ptp) REVERT: E 37 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7204 (ptt-90) REVERT: F 49 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (mm) REVERT: F 132 ARG cc_start: 0.7562 (pmm-80) cc_final: 0.6747 (pmt170) REVERT: G 98 GLU cc_start: 0.8597 (pm20) cc_final: 0.7998 (tt0) REVERT: G 102 GLU cc_start: 0.7919 (mp0) cc_final: 0.7411 (mp0) REVERT: H 13 LYS cc_start: 0.7179 (tttt) cc_final: 0.6837 (ttpt) REVERT: H 118 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7999 (m-90) REVERT: I 136 ARG cc_start: 0.8224 (tpm170) cc_final: 0.7055 (tpt90) REVERT: J 123 ASN cc_start: 0.7241 (t0) cc_final: 0.6888 (t0) REVERT: J 148 SER cc_start: 0.8664 (m) cc_final: 0.8391 (p) REVERT: K 8 LYS cc_start: 0.8337 (tmmt) cc_final: 0.8122 (ttmt) outliers start: 66 outliers final: 25 residues processed: 320 average time/residue: 0.5892 time to fit residues: 219.4989 Evaluate side-chains 286 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 97 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 218 optimal weight: 0.0170 chunk 79 optimal weight: 0.1980 overall best weight: 2.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN H 36 GLN J 283 GLN L 75 GLN L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102204 restraints weight = 85280.088| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.00 r_work: 0.3202 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25915 Z= 0.195 Angle : 0.877 12.326 36361 Z= 0.386 Chirality : 0.069 0.663 4345 Planarity : 0.004 0.062 3525 Dihedral : 15.084 173.192 6038 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.15 % Allowed : 22.48 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.17), residues: 2276 helix: 0.16 (0.20), residues: 738 sheet: -0.13 (0.28), residues: 350 loop : -2.60 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 122 TYR 0.032 0.002 TYR K 37 PHE 0.012 0.001 PHE K 72 TRP 0.010 0.001 TRP L 120 HIS 0.004 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (25915) covalent geometry : angle 0.87724 / 0.39 (36361) hydrogen bonds : bond 0.04885 / 2.49 ( 792) hydrogen bonds : angle 4.19693 / 1.73 ( 2067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 260 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7974 (pp) REVERT: B 119 GLU cc_start: 0.8535 (tp30) cc_final: 0.8249 (tp30) REVERT: B 393 ASP cc_start: 0.8298 (m-30) cc_final: 0.7869 (t70) REVERT: B 486 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7980 (mt-10) REVERT: B 584 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: B 626 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8332 (ttt-90) REVERT: B 684 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6664 (mtt) REVERT: B 811 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7273 (ptmt) REVERT: B 843 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8465 (t0) REVERT: D 142 MET cc_start: 0.8006 (ptt) cc_final: 0.7620 (ptp) REVERT: E 37 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7378 (ptt-90) REVERT: E 92 ASP cc_start: 0.8949 (m-30) cc_final: 0.8685 (m-30) REVERT: F 49 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8679 (mm) REVERT: F 118 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8384 (m-10) REVERT: F 132 ARG cc_start: 0.7620 (pmm-80) cc_final: 0.6745 (pmt170) REVERT: G 102 GLU cc_start: 0.7927 (mp0) cc_final: 0.7587 (mp0) REVERT: G 104 ILE cc_start: 0.8198 (pt) cc_final: 0.7873 (pp) REVERT: H 13 LYS cc_start: 0.7362 (tttt) cc_final: 0.7058 (ttpt) REVERT: H 118 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.8046 (m-90) REVERT: I 118 THR cc_start: 0.9012 (t) cc_final: 0.8673 (p) REVERT: I 136 ARG cc_start: 0.8355 (tpm170) cc_final: 0.7203 (tpt90) REVERT: J 123 ASN cc_start: 0.7253 (t0) cc_final: 0.7048 (t0) REVERT: J 136 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7783 (mmm160) REVERT: J 148 SER cc_start: 0.8714 (m) cc_final: 0.8448 (p) REVERT: K 8 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8099 (ttmt) REVERT: L 26 LYS cc_start: 0.8422 (tppt) cc_final: 0.8183 (tppt) outliers start: 66 outliers final: 35 residues processed: 303 average time/residue: 0.5773 time to fit residues: 204.5524 Evaluate side-chains 297 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 35 TYR Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 95 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 216 optimal weight: 0.7980 chunk 246 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 526 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 36 GLN J 283 GLN L 75 GLN L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106153 restraints weight = 71079.164| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.69 r_work: 0.3275 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25915 Z= 0.131 Angle : 0.808 11.185 36361 Z= 0.356 Chirality : 0.063 0.531 4345 Planarity : 0.004 0.060 3525 Dihedral : 14.995 174.654 6038 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.96 % Allowed : 23.10 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.18), residues: 2276 helix: 0.31 (0.21), residues: 744 sheet: 0.04 (0.28), residues: 361 loop : -2.51 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 122 TYR 0.027 0.001 TYR K 37 PHE 0.016 0.001 PHE K 72 TRP 0.010 0.001 TRP B 556 HIS 0.007 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25915) covalent geometry : angle 0.80787 / 0.36 (36361) hydrogen bonds : bond 0.03948 / 2.02 ( 792) hydrogen bonds : angle 4.00449 / 1.65 ( 2067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 274 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7892 (pp) REVERT: B 119 GLU cc_start: 0.8505 (tp30) cc_final: 0.8181 (tp30) REVERT: B 204 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5247 (mp) REVERT: B 393 ASP cc_start: 0.8256 (m-30) cc_final: 0.7830 (t70) REVERT: B 486 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7946 (mt-10) REVERT: B 626 ARG cc_start: 0.8787 (ttt-90) cc_final: 0.8168 (ttt-90) REVERT: B 684 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6752 (mtt) REVERT: B 728 ILE cc_start: 0.8497 (mm) cc_final: 0.8163 (mt) REVERT: B 811 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7290 (ptmt) REVERT: B 843 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8390 (t0) REVERT: B 849 ARG cc_start: 0.8457 (mtm110) cc_final: 0.7955 (ptp-170) REVERT: D 91 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8275 (pp20) REVERT: D 142 MET cc_start: 0.7979 (ptt) cc_final: 0.7665 (ptp) REVERT: E 37 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7216 (ptt-90) REVERT: E 92 ASP cc_start: 0.8913 (m-30) cc_final: 0.8639 (m-30) REVERT: F 49 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8634 (mm) REVERT: F 122 ARG cc_start: 0.8528 (mtm110) cc_final: 0.7878 (mtm110) REVERT: F 130 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: F 132 ARG cc_start: 0.7572 (pmm-80) cc_final: 0.6714 (pmt170) REVERT: G 97 ILE cc_start: 0.9091 (mm) cc_final: 0.8829 (mm) REVERT: G 98 GLU cc_start: 0.8619 (pm20) cc_final: 0.8040 (tt0) REVERT: G 102 GLU cc_start: 0.7916 (mp0) cc_final: 0.7572 (mp0) REVERT: H 7 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7940 (mtt90) REVERT: H 13 LYS cc_start: 0.7295 (tttt) cc_final: 0.7008 (ttpt) REVERT: H 118 TRP cc_start: 0.8527 (OUTLIER) cc_final: 0.8001 (m-90) REVERT: I 118 THR cc_start: 0.8999 (t) cc_final: 0.8662 (p) REVERT: J 123 ASN cc_start: 0.7214 (t0) cc_final: 0.6986 (t0) REVERT: J 136 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7685 (mmm160) REVERT: L 26 LYS cc_start: 0.8405 (tppt) cc_final: 0.8062 (tppt) outliers start: 62 outliers final: 34 residues processed: 314 average time/residue: 0.5882 time to fit residues: 215.5071 Evaluate side-chains 297 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain L residue 35 TYR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 235 optimal weight: 0.2980 chunk 178 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN D 231 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN H 70 ASN J 283 GLN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.142746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108666 restraints weight = 85177.408| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.09 r_work: 0.3308 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25915 Z= 0.115 Angle : 0.785 16.274 36361 Z= 0.345 Chirality : 0.059 0.494 4345 Planarity : 0.004 0.058 3525 Dihedral : 14.830 177.065 6038 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.58 % Allowed : 24.49 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2276 helix: 0.46 (0.21), residues: 748 sheet: 0.34 (0.29), residues: 352 loop : -2.43 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 122 TYR 0.024 0.001 TYR K 37 PHE 0.017 0.001 PHE K 72 TRP 0.014 0.001 TRP L 87 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (25915) covalent geometry : angle 0.78527 / 0.35 (36361) hydrogen bonds : bond 0.03476 / 1.79 ( 792) hydrogen bonds : angle 3.87681 / 1.61 ( 2067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8479 (tp30) cc_final: 0.8095 (tp30) REVERT: B 204 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.4432 (mt) REVERT: B 486 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7763 (mt-10) REVERT: B 626 ARG cc_start: 0.8816 (ttt-90) cc_final: 0.8233 (ttt-90) REVERT: B 684 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6707 (mtt) REVERT: B 811 LYS cc_start: 0.8072 (mmpt) cc_final: 0.7316 (ptmt) REVERT: B 843 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8408 (t0) REVERT: D 91 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8223 (pp20) REVERT: E 37 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7242 (ptt-90) REVERT: E 91 GLU cc_start: 0.8841 (pm20) cc_final: 0.8273 (pp20) REVERT: F 130 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: F 132 ARG cc_start: 0.7551 (pmm-80) cc_final: 0.6668 (pmt170) REVERT: G 97 ILE cc_start: 0.9055 (mm) cc_final: 0.8813 (mm) REVERT: G 98 GLU cc_start: 0.8604 (pm20) cc_final: 0.8061 (tt0) REVERT: G 102 GLU cc_start: 0.7955 (mp0) cc_final: 0.7418 (mp0) REVERT: H 118 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7988 (m-90) REVERT: I 64 ASP cc_start: 0.7748 (t0) cc_final: 0.7539 (t0) REVERT: I 118 THR cc_start: 0.8990 (t) cc_final: 0.8646 (p) REVERT: I 125 ASP cc_start: 0.7880 (m-30) cc_final: 0.6886 (t0) REVERT: I 136 ARG cc_start: 0.8482 (tpm170) cc_final: 0.7075 (tpt90) REVERT: J 123 ASN cc_start: 0.7204 (t0) cc_final: 0.6976 (t0) REVERT: J 136 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7676 (mmm160) REVERT: K 8 LYS cc_start: 0.7889 (tmmm) cc_final: 0.7510 (tmmt) REVERT: K 30 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7909 (mtt-85) REVERT: L 26 LYS cc_start: 0.8379 (tppt) cc_final: 0.8068 (tppt) outliers start: 54 outliers final: 26 residues processed: 318 average time/residue: 0.6154 time to fit residues: 227.7374 Evaluate side-chains 294 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain L residue 35 TYR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 241 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN J 283 GLN L 71 HIS L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108692 restraints weight = 68325.891| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.64 r_work: 0.3312 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25915 Z= 0.125 Angle : 0.794 13.829 36361 Z= 0.351 Chirality : 0.060 0.523 4345 Planarity : 0.004 0.073 3525 Dihedral : 14.761 177.590 6038 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.29 % Allowed : 25.39 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2276 helix: 0.53 (0.21), residues: 747 sheet: 0.36 (0.28), residues: 360 loop : -2.38 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 849 TYR 0.021 0.001 TYR I 160 PHE 0.015 0.001 PHE K 72 TRP 0.025 0.001 TRP L 87 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (25915) covalent geometry : angle 0.79404 / 0.35 (36361) hydrogen bonds : bond 0.03694 / 1.89 ( 792) hydrogen bonds : angle 3.85903 / 1.60 ( 2067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 MET cc_start: 0.8092 (mpp) cc_final: 0.7483 (mpp) REVERT: B 204 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.4363 (mt) REVERT: B 393 ASP cc_start: 0.8242 (m-30) cc_final: 0.7822 (t70) REVERT: B 486 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7747 (mt-10) REVERT: B 584 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8325 (ttp-170) REVERT: B 626 ARG cc_start: 0.8803 (ttt-90) cc_final: 0.8275 (ttt-90) REVERT: B 684 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6731 (mtt) REVERT: B 811 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7312 (ptmt) REVERT: B 843 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8384 (t0) REVERT: D 91 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8221 (pp20) REVERT: E 37 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7214 (ptt-90) REVERT: E 91 GLU cc_start: 0.8846 (pm20) cc_final: 0.8271 (pp20) REVERT: F 9 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: F 49 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8643 (mm) REVERT: F 130 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: F 132 ARG cc_start: 0.7539 (pmm-80) cc_final: 0.6652 (pmt170) REVERT: G 98 GLU cc_start: 0.8565 (pm20) cc_final: 0.8075 (tt0) REVERT: G 102 GLU cc_start: 0.7894 (mp0) cc_final: 0.7469 (mp0) REVERT: H 118 TRP cc_start: 0.8508 (OUTLIER) cc_final: 0.7930 (m-90) REVERT: I 118 THR cc_start: 0.9002 (t) cc_final: 0.8651 (p) REVERT: I 125 ASP cc_start: 0.7875 (m-30) cc_final: 0.6869 (t0) REVERT: I 136 ARG cc_start: 0.8488 (tpm170) cc_final: 0.7103 (tpt90) REVERT: J 123 ASN cc_start: 0.7179 (t0) cc_final: 0.6964 (t0) REVERT: K 8 LYS cc_start: 0.7898 (tmmm) cc_final: 0.7509 (tmmt) REVERT: L 119 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7661 (mp) outliers start: 48 outliers final: 30 residues processed: 295 average time/residue: 0.6498 time to fit residues: 221.9776 Evaluate side-chains 295 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 149 CYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain L residue 35 TYR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 184 optimal weight: 0.0040 chunk 129 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 237 optimal weight: 0.9980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN B 695 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108910 restraints weight = 79528.470| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.95 r_work: 0.3307 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25915 Z= 0.121 Angle : 0.793 13.575 36361 Z= 0.351 Chirality : 0.059 0.504 4345 Planarity : 0.004 0.089 3525 Dihedral : 14.744 177.876 6038 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.20 % Allowed : 25.82 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 2276 helix: 0.68 (0.21), residues: 734 sheet: 0.40 (0.29), residues: 358 loop : -2.30 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 849 TYR 0.023 0.001 TYR K 36 PHE 0.016 0.001 PHE J 140 TRP 0.022 0.001 TRP L 87 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25915) covalent geometry : angle 0.79330 / 0.35 (36361) hydrogen bonds : bond 0.03576 / 1.83 ( 792) hydrogen bonds : angle 3.83600 / 1.59 ( 2067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7984 (pp) REVERT: B 152 MET cc_start: 0.8035 (mpp) cc_final: 0.7441 (mpp) REVERT: B 204 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.4332 (mt) REVERT: B 393 ASP cc_start: 0.8266 (m-30) cc_final: 0.7836 (t70) REVERT: B 486 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7699 (mt-10) REVERT: B 584 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8347 (ttp-170) REVERT: B 626 ARG cc_start: 0.8832 (ttt-90) cc_final: 0.8301 (ttt-90) REVERT: B 684 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6668 (mtt) REVERT: B 811 LYS cc_start: 0.8057 (mmpt) cc_final: 0.7306 (ptmt) REVERT: B 843 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8371 (t0) REVERT: D 91 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8219 (pp20) REVERT: E 37 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7249 (ptt-90) REVERT: E 91 GLU cc_start: 0.8845 (pm20) cc_final: 0.8312 (pp20) REVERT: F 9 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: F 49 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (mm) REVERT: F 130 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: F 132 ARG cc_start: 0.7527 (pmm-80) cc_final: 0.6661 (pmt170) REVERT: G 66 LEU cc_start: 0.8242 (tt) cc_final: 0.8011 (tm) REVERT: G 98 GLU cc_start: 0.8560 (pm20) cc_final: 0.8096 (tt0) REVERT: G 102 GLU cc_start: 0.7893 (mp0) cc_final: 0.7457 (mp0) REVERT: H 118 TRP cc_start: 0.8584 (OUTLIER) cc_final: 0.7994 (m-90) REVERT: I 118 THR cc_start: 0.8992 (t) cc_final: 0.8642 (p) REVERT: I 125 ASP cc_start: 0.7892 (m-30) cc_final: 0.6877 (t0) REVERT: I 136 ARG cc_start: 0.8506 (tpm170) cc_final: 0.7138 (tpt90) REVERT: J 123 ASN cc_start: 0.7167 (t0) cc_final: 0.6952 (t0) REVERT: K 8 LYS cc_start: 0.7856 (tmmm) cc_final: 0.7460 (tmmt) REVERT: L 119 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7671 (mp) outliers start: 46 outliers final: 26 residues processed: 289 average time/residue: 0.6223 time to fit residues: 210.0233 Evaluate side-chains 293 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 38 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 61 optimal weight: 0.0060 chunk 193 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN B 695 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108461 restraints weight = 65114.212| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.53 r_work: 0.3310 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25915 Z= 0.135 Angle : 0.799 13.199 36361 Z= 0.354 Chirality : 0.060 0.529 4345 Planarity : 0.004 0.054 3525 Dihedral : 14.748 177.921 6038 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.29 % Allowed : 26.16 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2276 helix: 0.62 (0.21), residues: 741 sheet: 0.27 (0.28), residues: 371 loop : -2.30 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 849 TYR 0.048 0.001 TYR K 37 PHE 0.018 0.001 PHE K 72 TRP 0.023 0.001 TRP L 87 HIS 0.010 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (25915) covalent geometry : angle 0.79921 / 0.35 (36361) hydrogen bonds : bond 0.03767 / 1.93 ( 792) hydrogen bonds : angle 3.84819 / 1.60 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9214.94 seconds wall clock time: 157 minutes 40.20 seconds (9460.20 seconds total)