Starting phenix.real_space_refine on Fri Sep 19 09:18:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6v_21564/09_2025/6w6v_21564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6v_21564/09_2025/6w6v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2025/6w6v_21564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2025/6w6v_21564.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2025/6w6v_21564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6v_21564/09_2025/6w6v_21564.cif" } 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-2.0-5805/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 7.41, per 1000 atoms: 0.30 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.55 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: 5.56 Time building geometry restraints manager: 2.96 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: 36081 2.68 - 5.36: 252 5.36 - 8.04: 21 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 - 22.37: 14349 22.37 - 44.75: 1191 44.75 - 67.12: 467 67.12 - 89.49: 76 89.49 - 111.87: 5 Dihedral angle restraints: 16088 sinusoidal: 9327 harmonic: 6761 Sorted by residual: dihedral pdb=" CA VAL D 140 " pdb=" C VAL D 140 " pdb=" N PRO D 141 " pdb=" CA PRO D 141 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE D 207 " pdb=" C PHE D 207 " pdb=" N PHE D 208 " pdb=" CA PHE D 208 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ARG D 260 " pdb=" C ARG D 260 " pdb=" N ALA D 261 " pdb=" CA ALA D 261 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 16085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3358 0.044 - 0.088: 764 0.088 - 0.132: 192 0.132 - 0.176: 26 0.176 - 0.220: 5 Chirality restraints: 4345 Sorted by residual: chirality pdb=" CG LEU G 66 " pdb=" CB LEU G 66 " pdb=" CD1 LEU G 66 " pdb=" CD2 LEU G 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE B 700 " pdb=" CA ILE B 700 " pdb=" CG1 ILE B 700 " pdb=" CG2 ILE B 700 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1' A A 86 " pdb=" O4' A A 86 " pdb=" C2' A A 86 " pdb=" N9 A A 86 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.10e+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: 14.030 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: 0.050 Extract box with map and model: 0.660 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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= 0.175 Angle : 0.633 13.397 36361 Z= 0.350 Chirality : 0.041 0.220 4345 Planarity : 0.004 0.097 3525 Dihedral : 18.065 111.867 11698 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 aren 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 covalent geometry : bond 0.00381 (25915) covalent geometry : angle 0.63313 (36361) hydrogen bonds : bond 0.15780 ( 792) hydrogen bonds : angle 6.08986 ( 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 : 0.780 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: 0.6786 time to fit residues: 299.0577 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 : 0.777 ------------------------------------------------------------------------------- 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: 7.9990 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: 3.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099959 restraints weight = 71912.017| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.67 r_work: 0.3170 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1704 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= 0.220 Angle : 0.679 13.555 36361 Z= 0.349 Chirality : 0.043 0.179 4345 Planarity : 0.005 0.068 3525 Dihedral : 18.826 111.032 6986 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 2.86 % Allowed : 13.13 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.17), residues: 2276 helix: -0.29 (0.20), residues: 735 sheet: -0.39 (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 K 30 TYR 0.026 0.002 TYR I 160 PHE 0.022 0.002 PHE G 51 TRP 0.021 0.002 TRP L 87 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00496 (25915) covalent geometry : angle 0.67892 (36361) hydrogen bonds : bond 0.05668 ( 792) hydrogen bonds : angle 4.66829 ( 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 348 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 811 LYS cc_start: 0.8074 (mmpt) cc_final: 0.7358 (ptmt) REVERT: B 843 ASP cc_start: 0.8838 (t70) cc_final: 0.8440 (t70) REVERT: D 91 GLU cc_start: 0.7710 (pp20) cc_final: 0.7228 (tm-30) REVERT: D 268 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7918 (mtp85) REVERT: F 49 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8543 (mm) REVERT: F 122 ARG cc_start: 0.8622 (mtm110) cc_final: 0.8389 (mtm110) REVERT: F 130 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: F 132 ARG cc_start: 0.7350 (pmm-80) cc_final: 0.6670 (pmt170) REVERT: G 85 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7732 (tm-30) REVERT: G 102 GLU cc_start: 0.7768 (mp0) cc_final: 0.7485 (mp0) REVERT: G 104 ILE cc_start: 0.8300 (pt) cc_final: 0.7953 (pp) REVERT: H 13 LYS cc_start: 0.7165 (tttt) cc_final: 0.6868 (ttpt) REVERT: H 118 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.7942 (m-90) REVERT: I 136 ARG cc_start: 0.8059 (tpm170) cc_final: 0.6998 (tpt90) REVERT: I 200 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: J 123 ASN cc_start: 0.7033 (t0) cc_final: 0.6771 (t0) REVERT: J 136 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7623 (mtm180) REVERT: K 8 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8171 (tmmt) outliers start: 60 outliers final: 18 residues processed: 316 average time/residue: 0.6986 time to fit residues: 252.9819 Evaluate side-chains 277 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 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 20 SER Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 136 ARG 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 Chi-restraints excluded: chain L residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 171 optimal weight: 0.0030 chunk 135 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 236 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 180 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN 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 = 0.3861 r_free = 0.3861 target = 0.138211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104029 restraints weight = 102093.607| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.45 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25915 Z= 0.102 Angle : 0.565 13.402 36361 Z= 0.289 Chirality : 0.038 0.172 4345 Planarity : 0.004 0.059 3525 Dihedral : 18.591 114.142 6984 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.24 % Allowed : 16.28 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.17), residues: 2276 helix: 0.26 (0.21), residues: 729 sheet: 0.03 (0.29), residues: 343 loop : -2.62 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 849 TYR 0.025 0.001 TYR K 37 PHE 0.022 0.001 PHE K 72 TRP 0.011 0.001 TRP B 624 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00215 (25915) covalent geometry : angle 0.56458 (36361) hydrogen bonds : bond 0.03769 ( 792) hydrogen bonds : angle 4.15321 ( 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 362 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7865 (m-30) cc_final: 0.7296 (t70) REVERT: B 486 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7681 (mt-10) REVERT: B 550 ARG cc_start: 0.7073 (mtm180) cc_final: 0.6850 (mtm180) REVERT: B 626 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.7873 (ttt-90) REVERT: B 811 LYS cc_start: 0.8035 (mmpt) cc_final: 0.7407 (ptmt) REVERT: B 843 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7813 (t0) REVERT: B 849 ARG cc_start: 0.8350 (mtm110) cc_final: 0.7774 (ptp-170) REVERT: D 142 MET cc_start: 0.7690 (ptt) cc_final: 0.7257 (ptp) REVERT: F 49 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8522 (mm) REVERT: F 132 ARG cc_start: 0.7164 (pmm-80) cc_final: 0.6377 (pmt170) REVERT: G 70 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7390 (tptm) REVERT: G 85 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7591 (tm-30) REVERT: G 98 GLU cc_start: 0.8248 (pm20) cc_final: 0.7961 (tt0) REVERT: G 102 GLU cc_start: 0.7635 (mp0) cc_final: 0.7131 (mp0) REVERT: H 13 LYS cc_start: 0.6855 (tttt) cc_final: 0.6576 (ttpt) REVERT: H 118 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.7757 (m-90) REVERT: I 125 ASP cc_start: 0.7966 (m-30) cc_final: 0.6986 (t0) REVERT: J 123 ASN cc_start: 0.7051 (t0) cc_final: 0.6778 (t0) REVERT: K 8 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7980 (ttmt) outliers start: 47 outliers final: 16 residues processed: 339 average time/residue: 0.6281 time to fit residues: 247.0041 Evaluate side-chains 280 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 70 LYS 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: 4.9990 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 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: 3.9990 chunk 246 optimal weight: 0.0070 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN J 283 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 = 0.3775 r_free = 0.3775 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097614 restraints weight = 94994.768| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.20 r_work: 0.3118 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 25915 Z= 0.257 Angle : 0.699 11.424 36361 Z= 0.358 Chirality : 0.044 0.187 4345 Planarity : 0.005 0.068 3525 Dihedral : 18.664 110.594 6984 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 3.29 % Allowed : 18.76 % Favored : 77.95 % 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 aren not related in a simple way. whole: -2.07 (0.17), residues: 2276 helix: -0.09 (0.20), residues: 743 sheet: -0.22 (0.28), residues: 354 loop : -2.72 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 122 TYR 0.025 0.002 TYR H 84 PHE 0.014 0.002 PHE L 52 TRP 0.033 0.002 TRP L 87 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00583 (25915) covalent geometry : angle 0.69946 (36361) hydrogen bonds : bond 0.05860 ( 792) hydrogen bonds : angle 4.43823 ( 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 335 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 393 ASP cc_start: 0.8286 (m-30) cc_final: 0.7755 (t70) REVERT: B 486 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7990 (mt-10) REVERT: B 584 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8441 (ttp-170) REVERT: B 626 ARG cc_start: 0.8795 (ttt-90) cc_final: 0.8305 (ttt-90) REVERT: B 684 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6619 (mtt) REVERT: B 811 LYS cc_start: 0.8081 (mmpt) cc_final: 0.7289 (ptmt) REVERT: B 843 ASP cc_start: 0.8874 (t70) cc_final: 0.8504 (t0) REVERT: B 849 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8084 (ptp-170) REVERT: D 142 MET cc_start: 0.8028 (ptt) cc_final: 0.7646 (ptp) REVERT: D 268 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8048 (mtp85) REVERT: F 49 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8615 (mm) REVERT: F 130 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: F 132 ARG cc_start: 0.7481 (pmm-80) cc_final: 0.6691 (pmt170) REVERT: G 52 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8615 (mp) REVERT: G 70 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7699 (tptm) REVERT: G 85 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7858 (tm-30) REVERT: G 102 GLU cc_start: 0.7813 (mp0) cc_final: 0.7401 (mp0) REVERT: G 104 ILE cc_start: 0.8253 (pt) cc_final: 0.7927 (pp) REVERT: H 118 TRP cc_start: 0.8564 (OUTLIER) cc_final: 0.8027 (m-90) REVERT: I 136 ARG cc_start: 0.8270 (tpm170) cc_final: 0.7126 (tpt90) REVERT: J 123 ASN cc_start: 0.7243 (t0) cc_final: 0.6910 (t0) REVERT: J 282 GLU cc_start: 0.8236 (mp0) cc_final: 0.8024 (mp0) REVERT: K 8 LYS cc_start: 0.8338 (tmmt) cc_final: 0.8102 (ttmt) outliers start: 69 outliers final: 30 residues processed: 307 average time/residue: 0.6331 time to fit residues: 226.0451 Evaluate side-chains 282 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 684 MET Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain D residue 168 LEU 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 F residue 49 ILE Chi-restraints excluded: chain F residue 51 LYS 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 70 LYS 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 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 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 K residue 63 HIS 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: 1.9990 chunk 203 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 195 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 87 HIS 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 = 0.3840 r_free = 0.3840 target = 0.136634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102808 restraints weight = 84180.869| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.03 r_work: 0.3217 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25915 Z= 0.108 Angle : 0.571 9.477 36361 Z= 0.294 Chirality : 0.039 0.196 4345 Planarity : 0.004 0.060 3525 Dihedral : 18.474 113.442 6984 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.63 % Allowed : 20.48 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.18), residues: 2276 helix: 0.36 (0.21), residues: 737 sheet: 0.03 (0.28), residues: 351 loop : -2.56 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 122 TYR 0.031 0.001 TYR K 37 PHE 0.018 0.001 PHE K 72 TRP 0.016 0.001 TRP L 87 HIS 0.007 0.001 HIS L 71 Details of bonding type rmsd covalent geometry : bond 0.00234 (25915) covalent geometry : angle 0.57134 (36361) hydrogen bonds : bond 0.03840 ( 792) hydrogen bonds : angle 4.06443 ( 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 333 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B 393 ASP cc_start: 0.8242 (m-30) cc_final: 0.7743 (t70) REVERT: B 486 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7779 (mt-10) REVERT: B 626 ARG cc_start: 0.8808 (ttt-90) cc_final: 0.8237 (ttt-90) REVERT: B 684 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6862 (mtp) REVERT: B 811 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7292 (ptmt) REVERT: B 843 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8398 (t0) REVERT: B 849 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8105 (ptp-170) REVERT: D 142 MET cc_start: 0.7956 (ptt) cc_final: 0.7643 (ptp) REVERT: E 37 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7214 (ptt-90) REVERT: F 132 ARG cc_start: 0.7359 (pmm-80) cc_final: 0.6564 (pmt170) REVERT: G 70 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7694 (tptm) REVERT: G 85 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7734 (tm-30) REVERT: G 98 GLU cc_start: 0.8660 (pm20) cc_final: 0.8142 (tt0) REVERT: G 102 GLU cc_start: 0.7865 (mp0) cc_final: 0.7642 (mp0) REVERT: H 118 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.7971 (m-90) REVERT: I 124 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6699 (mm) REVERT: I 125 ASP cc_start: 0.7830 (m-30) cc_final: 0.6844 (t0) REVERT: J 123 ASN cc_start: 0.7155 (t0) cc_final: 0.6825 (t0) REVERT: J 148 SER cc_start: 0.8705 (m) cc_final: 0.8444 (p) REVERT: K 8 LYS cc_start: 0.8325 (tmmt) cc_final: 0.8096 (ttmt) REVERT: L 26 LYS cc_start: 0.8278 (tppt) cc_final: 0.8073 (tppt) outliers start: 55 outliers final: 21 residues processed: 308 average time/residue: 0.6425 time to fit residues: 228.4480 Evaluate side-chains 282 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 85 SER Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 117 VAL 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 G residue 70 LYS Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 124 LEU 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 260 VAL Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 63 HIS 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: 2.9990 chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 218 optimal weight: 0.0170 chunk 79 optimal weight: 2.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 129 GLN H 36 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3819 r_free = 0.3819 target = 0.135044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100723 restraints weight = 96202.430| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.27 r_work: 0.3175 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 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 = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25915 Z= 0.149 Angle : 0.601 10.063 36361 Z= 0.306 Chirality : 0.040 0.175 4345 Planarity : 0.004 0.059 3525 Dihedral : 18.422 112.391 6984 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.01 % Allowed : 21.86 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.18), residues: 2276 helix: 0.36 (0.21), residues: 738 sheet: 0.08 (0.29), residues: 343 loop : -2.54 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 122 TYR 0.025 0.001 TYR H 84 PHE 0.014 0.001 PHE K 72 TRP 0.015 0.001 TRP L 87 HIS 0.004 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00335 (25915) covalent geometry : angle 0.60090 (36361) hydrogen bonds : bond 0.04354 ( 792) hydrogen bonds : angle 4.07386 ( 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 332 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7940 (pp) REVERT: B 204 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5096 (mp) REVERT: B 393 ASP cc_start: 0.8291 (m-30) cc_final: 0.7834 (t70) REVERT: B 486 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7814 (mt-10) REVERT: B 626 ARG cc_start: 0.8830 (ttt-90) cc_final: 0.8376 (ttt-90) REVERT: B 684 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6892 (mtp) REVERT: B 811 LYS cc_start: 0.8068 (mmpt) cc_final: 0.7271 (ptmt) REVERT: B 843 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8452 (t0) REVERT: D 142 MET cc_start: 0.8062 (ptt) cc_final: 0.7754 (ptp) REVERT: E 3 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7588 (ptt180) REVERT: E 37 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7232 (ptt-90) REVERT: E 92 ASP cc_start: 0.8943 (m-30) cc_final: 0.8683 (m-30) REVERT: F 49 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8620 (mm) REVERT: F 132 ARG cc_start: 0.7453 (pmm-80) cc_final: 0.6618 (pmt170) REVERT: G 70 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7745 (tptm) REVERT: G 85 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7793 (tm-30) REVERT: G 98 GLU cc_start: 0.8611 (pm20) cc_final: 0.8125 (tt0) REVERT: G 102 GLU cc_start: 0.7864 (mp0) cc_final: 0.7606 (mp0) REVERT: H 118 TRP cc_start: 0.8556 (OUTLIER) cc_final: 0.8017 (m-90) REVERT: I 125 ASP cc_start: 0.7892 (m-30) cc_final: 0.6895 (t0) REVERT: J 73 MET cc_start: 0.8825 (mmm) cc_final: 0.8514 (mmm) REVERT: J 123 ASN cc_start: 0.7228 (t0) cc_final: 0.6898 (t0) REVERT: J 136 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7750 (mmm160) REVERT: J 148 SER cc_start: 0.8690 (m) cc_final: 0.8442 (p) REVERT: K 8 LYS cc_start: 0.8274 (tmmt) cc_final: 0.8044 (ttmt) REVERT: K 37 TYR cc_start: 0.8531 (t80) cc_final: 0.8328 (t80) REVERT: L 26 LYS cc_start: 0.8447 (tppt) cc_final: 0.8072 (tppt) outliers start: 63 outliers final: 31 residues processed: 306 average time/residue: 0.5969 time to fit residues: 211.9113 Evaluate side-chains 299 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 799 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 3 ARG 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 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 G residue 70 LYS 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 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 K residue 63 HIS Chi-restraints excluded: chain K residue 73 ASN 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: 7.9990 chunk 206 optimal weight: 0.0870 chunk 205 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 526 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 111 GLN H 36 GLN H 70 ASN J 283 GLN L 75 GLN L 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.138321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104661 restraints weight = 77609.184| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.89 r_work: 0.3250 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25915 Z= 0.104 Angle : 0.569 9.376 36361 Z= 0.290 Chirality : 0.038 0.172 4345 Planarity : 0.004 0.056 3525 Dihedral : 18.324 113.739 6984 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.58 % Allowed : 23.10 % Favored : 74.32 % 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 aren not related in a simple way. whole: -1.44 (0.18), residues: 2276 helix: 0.53 (0.21), residues: 737 sheet: 0.35 (0.29), residues: 343 loop : -2.45 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 849 TYR 0.021 0.001 TYR I 160 PHE 0.018 0.001 PHE K 72 TRP 0.012 0.001 TRP L 87 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00231 (25915) covalent geometry : angle 0.56886 (36361) hydrogen bonds : bond 0.03495 ( 792) hydrogen bonds : angle 3.90044 ( 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 333 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 MET cc_start: 0.7975 (mpp) cc_final: 0.7285 (mpp) REVERT: B 393 ASP cc_start: 0.8251 (m-30) cc_final: 0.7802 (t70) REVERT: B 486 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7704 (mt-10) REVERT: B 626 ARG cc_start: 0.8839 (ttt-90) cc_final: 0.8279 (ttt-90) REVERT: B 684 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6893 (mtp) REVERT: B 811 LYS cc_start: 0.8081 (mmpt) cc_final: 0.7346 (ptmt) REVERT: B 843 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8396 (t0) REVERT: D 91 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8215 (pp20) REVERT: D 142 MET cc_start: 0.7993 (ptt) cc_final: 0.7728 (ptp) REVERT: E 92 ASP cc_start: 0.8899 (m-30) cc_final: 0.8645 (m-30) REVERT: F 9 GLU cc_start: 0.8354 (pm20) cc_final: 0.7792 (pm20) REVERT: F 49 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8602 (mm) REVERT: F 130 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: F 132 ARG cc_start: 0.7374 (pmm-80) cc_final: 0.6573 (pmt170) REVERT: G 70 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7660 (tptm) REVERT: G 85 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7729 (tm-30) REVERT: G 98 GLU cc_start: 0.8544 (pm20) cc_final: 0.8111 (tt0) REVERT: G 102 GLU cc_start: 0.7876 (mp0) cc_final: 0.7490 (mp0) REVERT: H 118 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7946 (m-90) REVERT: I 124 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6663 (mm) REVERT: I 125 ASP cc_start: 0.7840 (m-30) cc_final: 0.6791 (t0) REVERT: I 136 ARG cc_start: 0.8429 (tpm170) cc_final: 0.7008 (tpt90) REVERT: J 73 MET cc_start: 0.8821 (mmm) cc_final: 0.8524 (mmm) REVERT: J 123 ASN cc_start: 0.7148 (t0) cc_final: 0.6847 (t0) REVERT: J 136 ARG cc_start: 0.7958 (mmm160) cc_final: 0.7728 (mmm160) REVERT: J 148 SER cc_start: 0.8676 (m) cc_final: 0.8447 (p) REVERT: K 30 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7544 (ppt-90) outliers start: 54 outliers final: 29 residues processed: 315 average time/residue: 0.6265 time to fit residues: 228.5883 Evaluate side-chains 297 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 49 ILE 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 F residue 148 ILE Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 124 LEU 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 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 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: 7.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 222 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 40 ASN J 283 GLN L 71 HIS L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103215 restraints weight = 99399.229| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.37 r_work: 0.3212 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2936 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= 0.117 Angle : 0.587 15.857 36361 Z= 0.296 Chirality : 0.038 0.174 4345 Planarity : 0.004 0.058 3525 Dihedral : 18.279 113.196 6984 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.05 % Allowed : 23.58 % Favored : 73.37 % 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 aren not related in a simple way. whole: -1.38 (0.18), residues: 2276 helix: 0.50 (0.21), residues: 746 sheet: 0.39 (0.29), residues: 343 loop : -2.38 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 849 TYR 0.032 0.001 TYR K 37 PHE 0.014 0.001 PHE K 72 TRP 0.012 0.001 TRP L 87 HIS 0.007 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00264 (25915) covalent geometry : angle 0.58683 (36361) hydrogen bonds : bond 0.03717 ( 792) hydrogen bonds : angle 3.87720 ( 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 335 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.4255 (mt) REVERT: B 393 ASP cc_start: 0.8285 (m-30) cc_final: 0.7849 (t70) REVERT: B 486 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7729 (mt-10) REVERT: B 584 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8375 (ttp-170) REVERT: B 626 ARG cc_start: 0.8873 (ttt-90) cc_final: 0.8343 (ttt-90) REVERT: B 636 GLU cc_start: 0.8219 (pm20) cc_final: 0.7736 (pm20) REVERT: B 684 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6891 (mtp) REVERT: B 811 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7343 (ptmt) REVERT: B 843 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8421 (t0) REVERT: D 91 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8249 (pp20) REVERT: E 3 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7328 (ptt180) REVERT: E 37 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7220 (ptt-90) REVERT: E 91 GLU cc_start: 0.8920 (pm20) cc_final: 0.8306 (pp20) REVERT: F 49 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8626 (mm) REVERT: F 130 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: F 132 ARG cc_start: 0.7311 (pmm-80) cc_final: 0.6504 (pmt170) REVERT: G 70 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7736 (tptm) REVERT: G 85 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7735 (tm-30) REVERT: G 98 GLU cc_start: 0.8556 (pm20) cc_final: 0.8117 (tt0) REVERT: G 102 GLU cc_start: 0.7910 (mp0) cc_final: 0.7638 (mp0) REVERT: H 118 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.7963 (m-90) REVERT: I 64 ASP cc_start: 0.7704 (t0) cc_final: 0.7486 (t0) REVERT: I 124 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6631 (mm) REVERT: I 125 ASP cc_start: 0.7904 (m-30) cc_final: 0.6862 (t0) REVERT: I 136 ARG cc_start: 0.8519 (tpm170) cc_final: 0.7074 (tpt90) REVERT: J 38 TYR cc_start: 0.7976 (m-80) cc_final: 0.7701 (m-80) REVERT: J 148 SER cc_start: 0.8675 (m) cc_final: 0.8458 (p) REVERT: K 8 LYS cc_start: 0.7949 (tmmm) cc_final: 0.7563 (tmmt) REVERT: L 119 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7674 (mp) outliers start: 64 outliers final: 31 residues processed: 309 average time/residue: 0.6187 time to fit residues: 222.3057 Evaluate side-chains 302 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 3 ARG 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 49 ILE 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 42 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 205 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 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 119 LEU 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: 10.0000 chunk 7 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 40 ASN H 128 GLN J 123 ASN J 283 GLN L 71 HIS L 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103026 restraints weight = 79357.765| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.92 r_work: 0.3218 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2978 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= 0.134 Angle : 0.612 14.308 36361 Z= 0.309 Chirality : 0.039 0.175 4345 Planarity : 0.004 0.056 3525 Dihedral : 18.260 112.985 6984 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.67 % Allowed : 24.30 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.18), residues: 2276 helix: 0.50 (0.21), residues: 747 sheet: 0.32 (0.29), residues: 353 loop : -2.38 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 849 TYR 0.030 0.001 TYR K 37 PHE 0.014 0.001 PHE B 491 TRP 0.013 0.001 TRP L 87 HIS 0.007 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00303 (25915) covalent geometry : angle 0.61242 (36361) hydrogen bonds : bond 0.03959 ( 792) hydrogen bonds : angle 3.91244 ( 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 316 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7924 (pp) REVERT: B 152 MET cc_start: 0.7946 (mpp) cc_final: 0.7221 (mpp) REVERT: B 204 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.4214 (mt) REVERT: B 393 ASP cc_start: 0.8276 (m-30) cc_final: 0.7862 (t70) REVERT: B 486 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7753 (mt-10) REVERT: B 550 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7359 (mpp80) REVERT: B 584 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8367 (ttp-170) REVERT: B 626 ARG cc_start: 0.8846 (ttt-90) cc_final: 0.8224 (ttt-90) REVERT: B 728 ILE cc_start: 0.8414 (mm) cc_final: 0.8053 (mt) REVERT: B 811 LYS cc_start: 0.8064 (mmpt) cc_final: 0.7265 (ptmt) REVERT: B 843 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8379 (t0) REVERT: D 91 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8238 (pp20) REVERT: D 142 MET cc_start: 0.7824 (ptt) cc_final: 0.7500 (ptp) REVERT: E 3 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7351 (ptt180) REVERT: E 37 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7196 (ptt180) REVERT: E 91 GLU cc_start: 0.8918 (pm20) cc_final: 0.8326 (pp20) REVERT: F 49 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8634 (mm) REVERT: F 130 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: G 70 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7756 (tptm) REVERT: G 85 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7744 (tm-30) REVERT: G 98 GLU cc_start: 0.8518 (pm20) cc_final: 0.8126 (tt0) REVERT: G 102 GLU cc_start: 0.7877 (mp0) cc_final: 0.7600 (mp0) REVERT: H 118 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7960 (m-90) REVERT: I 64 ASP cc_start: 0.7726 (t0) cc_final: 0.7525 (t0) REVERT: I 124 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6650 (mm) REVERT: I 125 ASP cc_start: 0.7890 (m-30) cc_final: 0.6815 (t0) REVERT: I 136 ARG cc_start: 0.8547 (tpm170) cc_final: 0.7167 (tpt90) REVERT: J 148 SER cc_start: 0.8656 (m) cc_final: 0.8440 (p) REVERT: K 8 LYS cc_start: 0.7944 (tmmm) cc_final: 0.7553 (tmmt) REVERT: K 22 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6596 (m170) REVERT: L 119 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7695 (mp) outliers start: 56 outliers final: 32 residues processed: 295 average time/residue: 0.6553 time to fit residues: 223.6218 Evaluate side-chains 301 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 584 ARG Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 3 ARG 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 49 ILE 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 42 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 124 LEU 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 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 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 22 HIS 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 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: 5.9990 chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 18 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN J 283 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 = 0.3850 r_free = 0.3850 target = 0.137494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103381 restraints weight = 85241.516| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.08 r_work: 0.3221 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- 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: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 11 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3040 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= 0.122 Angle : 0.612 14.110 36361 Z= 0.307 Chirality : 0.038 0.174 4345 Planarity : 0.004 0.055 3525 Dihedral : 18.239 113.242 6984 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.58 % Allowed : 24.44 % Favored : 72.98 % 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 aren not related in a simple way. whole: -1.31 (0.18), residues: 2276 helix: 0.62 (0.21), residues: 734 sheet: 0.29 (0.28), residues: 359 loop : -2.34 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 849 TYR 0.022 0.001 TYR K 36 PHE 0.015 0.001 PHE B 491 TRP 0.013 0.001 TRP L 87 HIS 0.006 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00274 (25915) covalent geometry : angle 0.61181 (36361) hydrogen bonds : bond 0.03793 ( 792) hydrogen bonds : angle 3.88521 ( 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 315 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 MET cc_start: 0.7990 (mpp) cc_final: 0.7224 (mpp) REVERT: B 204 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.4225 (mt) REVERT: B 393 ASP cc_start: 0.8269 (m-30) cc_final: 0.7801 (t70) REVERT: B 486 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7747 (mt-10) REVERT: B 584 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8377 (ttp-170) REVERT: B 626 ARG cc_start: 0.8854 (ttt-90) cc_final: 0.8214 (ttt-90) REVERT: B 636 GLU cc_start: 0.8219 (pm20) cc_final: 0.7781 (pm20) REVERT: B 811 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7252 (ptmt) REVERT: B 843 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (t0) REVERT: D 91 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8216 (pp20) REVERT: E 3 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7256 (ptt180) REVERT: E 37 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7212 (ptt180) REVERT: E 91 GLU cc_start: 0.8934 (pm20) cc_final: 0.8380 (pp20) REVERT: F 49 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8624 (mm) REVERT: F 130 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: F 132 ARG cc_start: 0.7318 (pmm-80) cc_final: 0.6482 (pmt170) REVERT: G 70 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7738 (tptm) REVERT: G 85 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7742 (tm-30) REVERT: G 98 GLU cc_start: 0.8513 (pm20) cc_final: 0.8115 (tt0) REVERT: G 102 GLU cc_start: 0.7885 (mp0) cc_final: 0.7601 (mp0) REVERT: H 118 TRP cc_start: 0.8540 (OUTLIER) cc_final: 0.7939 (m-90) REVERT: I 64 ASP cc_start: 0.7723 (t0) cc_final: 0.7498 (t0) REVERT: I 124 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6632 (mm) REVERT: I 125 ASP cc_start: 0.7866 (m-30) cc_final: 0.6772 (t0) REVERT: I 136 ARG cc_start: 0.8573 (tpm170) cc_final: 0.7185 (tpt90) REVERT: J 148 SER cc_start: 0.8661 (m) cc_final: 0.8445 (p) REVERT: K 8 LYS cc_start: 0.7919 (tmmm) cc_final: 0.7523 (tmmt) REVERT: L 119 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7675 (mp) outliers start: 54 outliers final: 32 residues processed: 295 average time/residue: 0.6588 time to fit residues: 225.1978 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 : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 LEU 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 584 ARG 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 3 ARG 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 49 ILE 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 42 VAL 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 70 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 124 LEU 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 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 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 63 HIS 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 38 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 190 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** E 59 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 = 0.3800 r_free = 0.3800 target = 0.133727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099833 restraints weight = 78819.060| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.87 r_work: 0.3166 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25915 Z= 0.201 Angle : 0.678 14.243 36361 Z= 0.342 Chirality : 0.042 0.305 4345 Planarity : 0.004 0.062 3525 Dihedral : 18.305 111.738 6984 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.82 % Allowed : 24.20 % Favored : 72.98 % 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 aren not related in a simple way. whole: -1.54 (0.18), residues: 2276 helix: 0.42 (0.21), residues: 739 sheet: -0.00 (0.28), residues: 366 loop : -2.43 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 849 TYR 0.026 0.002 TYR H 84 PHE 0.015 0.001 PHE K 72 TRP 0.017 0.001 TRP L 87 HIS 0.009 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00455 (25915) covalent geometry : angle 0.67815 (36361) hydrogen bonds : bond 0.04991 ( 792) hydrogen bonds : angle 4.09430 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9436.72 seconds wall clock time: 161 minutes 25.87 seconds (9685.87 seconds total)