Starting phenix.real_space_refine on Thu Mar 5 05:15:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xn4_22267/03_2026/6xn4_22267.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xn4_22267/03_2026/6xn4_22267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xn4_22267/03_2026/6xn4_22267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xn4_22267/03_2026/6xn4_22267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xn4_22267/03_2026/6xn4_22267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xn4_22267/03_2026/6xn4_22267.map" } resolution = 3.35 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= 0.003 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 64 5.49 5 S 48 5.16 5 C 12041 2.51 5 N 3263 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19273 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2227 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 275, 2225 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2272 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 736 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 25} Chain: "A" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5984 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Time building chain proxies: 4.87, per 1000 atoms: 0.25 Number of scatterers: 19273 At special positions: 0 Unit cell: (109.548, 126.732, 183.654, 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 48 16.00 P 64 15.00 O 3857 8.00 N 3263 7.00 C 12041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.01 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 894.2 milliseconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 40.5% alpha, 12.8% beta 2 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.582A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.555A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.073A pdb=" N LEU B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 removed outlier: 3.543A pdb=" N LEU F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.600A pdb=" N GLY F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 removed outlier: 3.546A pdb=" N ARG F 183 " --> pdb=" O HIS F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 157 through 174 removed outlier: 3.537A pdb=" N ASN H 164 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 166 " --> pdb=" O PHE H 162 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.797A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.539A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.732A pdb=" N GLU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 53 through 73 removed outlier: 4.369A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.554A pdb=" N ALA D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.621A pdb=" N THR D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.506A pdb=" N TYR D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.657A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 4.300A pdb=" N LYS A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 85 removed outlier: 4.116A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.801A pdb=" N LYS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.522A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.848A pdb=" N VAL A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 224 removed outlier: 3.597A pdb=" N HIS A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 270 through 295 removed outlier: 4.081A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 364 through 381 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.878A pdb=" N SER A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.931A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.679A pdb=" N GLU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 540 through 564 removed outlier: 3.920A pdb=" N THR A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.391A pdb=" N ASP A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.710A pdb=" N ASP A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 674 through 682 removed outlier: 3.522A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.654A pdb=" N GLY A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.574A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.514A pdb=" N THR J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 65 removed outlier: 3.803A pdb=" N VAL J 62 " --> pdb=" O PHE J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 127 through 138 removed outlier: 3.684A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.637A pdb=" N ALA J 154 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 229 removed outlier: 3.650A pdb=" N ILE J 213 " --> pdb=" O THR J 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP J 228 " --> pdb=" O TYR J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 301 removed outlier: 4.047A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 292 " --> pdb=" O ARG J 288 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 99 removed outlier: 3.649A pdb=" N PHE B 65 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 7 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 277 removed outlier: 5.858A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 94 through 96 removed outlier: 7.675A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AA9, first strand: chain 'H' and resid 94 through 95 removed outlier: 3.723A pdb=" N PHE H 146 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AB3, first strand: chain 'G' and resid 94 through 95 removed outlier: 6.447A pdb=" N VAL G 4 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL G 195 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU G 6 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 193 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.804A pdb=" N PHE C 42 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 304 through 305 removed outlier: 4.215A pdb=" N PHE A 247 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 352 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 249 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AC1, first strand: chain 'A' and resid 568 through 570 removed outlier: 3.518A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AC3, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC4, first strand: chain 'J' and resid 22 through 23 removed outlier: 6.666A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN J 173 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 37 through 40 removed outlier: 3.897A pdb=" N TYR J 86 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 314 through 315 729 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6115 1.34 - 1.48: 5333 1.48 - 1.62: 8202 1.62 - 1.76: 4 1.76 - 1.89: 88 Bond restraints: 19742 Sorted by residual: bond pdb=" CA ASN J 141 " pdb=" C ASN J 141 " ideal model delta sigma weight residual 1.522 1.436 0.087 1.37e-02 5.33e+03 4.00e+01 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.15e-02 7.56e+03 1.28e+01 bond pdb=" C LYS J 170 " pdb=" N VAL J 171 " ideal model delta sigma weight residual 1.329 1.289 0.040 1.46e-02 4.69e+03 7.61e+00 bond pdb=" CG1 ILE A 708 " pdb=" CD1 ILE A 708 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.45e+00 bond pdb=" C GLN J 259 " pdb=" N PRO J 260 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.19e-02 7.06e+03 7.37e+00 ... (remaining 19737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 26473 4.07 - 8.15: 381 8.15 - 12.22: 30 12.22 - 16.30: 3 16.30 - 20.37: 1 Bond angle restraints: 26888 Sorted by residual: angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.77 -20.37 2.30e+00 1.89e-01 7.84e+01 angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 123.91 136.92 -13.01 1.66e+00 3.63e-01 6.14e+01 angle pdb=" N ILE J 17 " pdb=" CA ILE J 17 " pdb=" C ILE J 17 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.53e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 107.52 6.19 9.50e-01 1.11e+00 4.24e+01 angle pdb=" N VAL A 199 " pdb=" CA VAL A 199 " pdb=" C VAL A 199 " ideal model delta sigma weight residual 113.10 107.33 5.77 9.70e-01 1.06e+00 3.54e+01 ... (remaining 26883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 11568 34.63 - 69.25: 374 69.25 - 103.88: 38 103.88 - 138.50: 4 138.50 - 173.13: 2 Dihedral angle restraints: 11986 sinusoidal: 5486 harmonic: 6500 Sorted by residual: dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual 180.00 46.16 133.84 0 5.00e+00 4.00e-02 7.16e+02 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual 180.00 116.21 63.79 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA ILE G 26 " pdb=" C ILE G 26 " pdb=" N GLY G 27 " pdb=" CA GLY G 27 " ideal model delta harmonic sigma weight residual 180.00 120.81 59.19 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 11983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2711 0.100 - 0.200: 299 0.200 - 0.300: 33 0.300 - 0.399: 4 0.399 - 0.499: 3 Chirality restraints: 3050 Sorted by residual: chirality pdb=" CB ILE A 708 " pdb=" CA ILE A 708 " pdb=" CG1 ILE A 708 " pdb=" CG2 ILE A 708 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CB VAL B 131 " pdb=" CA VAL B 131 " pdb=" CG1 VAL B 131 " pdb=" CG2 VAL B 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C1' A T 29 " pdb=" O4' A T 29 " pdb=" C2' A T 29 " pdb=" N9 A T 29 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3047 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 15 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C MET H 15 " 0.065 2.00e-02 2.50e+03 pdb=" O MET H 15 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS H 16 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 137 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" CD GLU C 137 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 137 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 15 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C MET G 15 " 0.056 2.00e-02 2.50e+03 pdb=" O MET G 15 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS G 16 " -0.018 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1373 2.71 - 3.26: 19283 3.26 - 3.81: 34177 3.81 - 4.35: 41684 4.35 - 4.90: 68043 Nonbonded interactions: 164560 Sorted by model distance: nonbonded pdb=" OG SER B 128 " pdb=" OH TYR B 186 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR B 232 " pdb=" O TYR A 383 " model vdw 2.200 3.040 nonbonded pdb=" OG SER F 47 " pdb=" OP1 A R 9 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OP2 U T 22 " model vdw 2.240 3.040 nonbonded pdb=" OG SER H 47 " pdb=" OP1 A R 21 " model vdw 2.243 3.040 ... (remaining 164555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 12 through 146) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) } 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=0.50 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: 1.470 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.009 0.106 19745 Z= 0.409 Angle : 1.247 20.371 26894 Z= 0.681 Chirality : 0.067 0.499 3050 Planarity : 0.006 0.052 3212 Dihedral : 17.199 173.125 7793 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.04 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.15), residues: 2202 helix: -2.11 (0.15), residues: 827 sheet: -1.71 (0.27), residues: 323 loop : -2.70 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 134 TYR 0.036 0.004 TYR J 283 PHE 0.049 0.004 PHE J 255 TRP 0.024 0.003 TRP A 186 HIS 0.009 0.002 HIS J 282 Details of bonding type rmsd covalent geometry : bond 0.00893 (19742) covalent geometry : angle 1.23804 (26888) SS BOND : bond 0.01710 ( 3) SS BOND : angle 9.81106 ( 6) hydrogen bonds : bond 0.19668 ( 733) hydrogen bonds : angle 8.48547 ( 2111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: F 120 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6603 (mm-30) REVERT: H 55 TYR cc_start: 0.8762 (t80) cc_final: 0.8487 (t80) REVERT: A 86 MET cc_start: 0.2028 (mpp) cc_final: 0.1611 (mpp) REVERT: A 250 MET cc_start: 0.8612 (tmm) cc_final: 0.8124 (tmm) REVERT: A 447 MET cc_start: 0.8166 (ptt) cc_final: 0.7550 (ptt) REVERT: A 453 MET cc_start: 0.8017 (ttm) cc_final: 0.7631 (ttm) REVERT: A 580 MET cc_start: 0.7654 (mtm) cc_final: 0.7385 (mtm) REVERT: J 292 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7938 (tpp80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1256 time to fit residues: 22.2673 Evaluate side-chains 81 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 HIS H 124 ASN H 192 ASN A 251 ASN A 355 ASN J 74 ASN J 92 GLN J 111 ASN J 141 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.080918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.063599 restraints weight = 86012.487| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.45 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19745 Z= 0.166 Angle : 0.710 19.221 26894 Z= 0.377 Chirality : 0.044 0.246 3050 Planarity : 0.004 0.055 3212 Dihedral : 16.450 160.977 3392 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.40 % Favored : 92.42 % Rotamer: Outliers : 0.57 % Allowed : 6.76 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2202 helix: -0.99 (0.16), residues: 849 sheet: -1.64 (0.24), residues: 375 loop : -2.59 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 311 TYR 0.017 0.002 TYR A 77 PHE 0.039 0.002 PHE A 36 TRP 0.012 0.002 TRP A 186 HIS 0.005 0.001 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00349 (19742) covalent geometry : angle 0.69471 (26888) SS BOND : bond 0.01988 ( 3) SS BOND : angle 9.88929 ( 6) hydrogen bonds : bond 0.04534 ( 733) hydrogen bonds : angle 5.98668 ( 2111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.688 Fit side-chains REVERT: A 86 MET cc_start: 0.2184 (mpp) cc_final: 0.1633 (mpp) REVERT: A 250 MET cc_start: 0.8578 (tmm) cc_final: 0.8141 (tmm) REVERT: A 453 MET cc_start: 0.8244 (ttm) cc_final: 0.7947 (ttt) REVERT: J 292 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7817 (tpp80) outliers start: 11 outliers final: 4 residues processed: 109 average time/residue: 0.1307 time to fit residues: 23.3491 Evaluate side-chains 86 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain A residue 8 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 53 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN B 208 ASN F 131 ASN H 121 ASN G 16 HIS ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS J 63 ASN J 282 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.078195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.062043 restraints weight = 120097.726| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.60 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 19745 Z= 0.318 Angle : 0.803 19.869 26894 Z= 0.424 Chirality : 0.047 0.314 3050 Planarity : 0.005 0.059 3212 Dihedral : 16.686 164.028 3392 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.90 % Favored : 89.96 % Rotamer: Outliers : 1.24 % Allowed : 11.62 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.16), residues: 2202 helix: -0.59 (0.17), residues: 848 sheet: -1.62 (0.25), residues: 358 loop : -2.57 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.021 0.002 TYR J 283 PHE 0.024 0.002 PHE A 36 TRP 0.013 0.002 TRP A 186 HIS 0.007 0.002 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00686 (19742) covalent geometry : angle 0.78810 (26888) SS BOND : bond 0.02427 ( 3) SS BOND : angle 10.39873 ( 6) hydrogen bonds : bond 0.04727 ( 733) hydrogen bonds : angle 5.91568 ( 2111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.865 Fit side-chains REVERT: B 94 LYS cc_start: 0.8347 (pttm) cc_final: 0.7785 (mtpt) REVERT: G 53 MET cc_start: 0.8765 (mtp) cc_final: 0.8564 (ttt) REVERT: A 86 MET cc_start: 0.2753 (mpp) cc_final: 0.2212 (mpp) REVERT: A 250 MET cc_start: 0.8619 (tmm) cc_final: 0.8282 (tmm) outliers start: 24 outliers final: 8 residues processed: 103 average time/residue: 0.1098 time to fit residues: 19.3862 Evaluate side-chains 85 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 302 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 211 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.081567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.065674 restraints weight = 114118.586| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 4.46 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19745 Z= 0.123 Angle : 0.637 18.845 26894 Z= 0.335 Chirality : 0.042 0.215 3050 Planarity : 0.004 0.055 3212 Dihedral : 16.016 159.258 3392 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 1.39 % Allowed : 12.44 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.17), residues: 2202 helix: -0.15 (0.18), residues: 851 sheet: -1.55 (0.25), residues: 378 loop : -2.54 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 311 TYR 0.015 0.001 TYR A 77 PHE 0.017 0.001 PHE A 36 TRP 0.020 0.001 TRP A 186 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00257 (19742) covalent geometry : angle 0.61935 (26888) SS BOND : bond 0.02274 ( 3) SS BOND : angle 9.87522 ( 6) hydrogen bonds : bond 0.03789 ( 733) hydrogen bonds : angle 5.36120 ( 2111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5087 (ttm) cc_final: 0.4872 (ttt) REVERT: A 75 ILE cc_start: 0.8379 (mm) cc_final: 0.7967 (mp) REVERT: A 86 MET cc_start: 0.2123 (mpp) cc_final: 0.1779 (mtt) outliers start: 27 outliers final: 10 residues processed: 116 average time/residue: 0.1250 time to fit residues: 23.7101 Evaluate side-chains 97 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 105 optimal weight: 0.0040 chunk 110 optimal weight: 0.8980 chunk 131 optimal weight: 40.0000 chunk 163 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.081859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.064290 restraints weight = 100846.504| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 4.81 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19745 Z= 0.124 Angle : 0.613 18.537 26894 Z= 0.322 Chirality : 0.042 0.195 3050 Planarity : 0.003 0.057 3212 Dihedral : 15.772 159.320 3392 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.63 % Favored : 92.23 % Rotamer: Outliers : 1.50 % Allowed : 14.20 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2202 helix: 0.07 (0.18), residues: 851 sheet: -1.41 (0.25), residues: 372 loop : -2.42 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 134 TYR 0.014 0.001 TYR B 232 PHE 0.014 0.001 PHE A 36 TRP 0.015 0.001 TRP A 186 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00262 (19742) covalent geometry : angle 0.59549 (26888) SS BOND : bond 0.02237 ( 3) SS BOND : angle 9.79189 ( 6) hydrogen bonds : bond 0.03646 ( 733) hydrogen bonds : angle 5.14286 ( 2111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 208 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6053 (mm) REVERT: C 62 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 109 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7623 (tm-30) REVERT: A 75 ILE cc_start: 0.8188 (mm) cc_final: 0.7578 (mt) REVERT: A 142 PRO cc_start: 0.4996 (Cg_exo) cc_final: 0.4722 (Cg_endo) outliers start: 29 outliers final: 16 residues processed: 116 average time/residue: 0.1161 time to fit residues: 22.3145 Evaluate side-chains 107 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 76 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 219 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS A 70 ASN ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.079096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.061366 restraints weight = 93814.988| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.57 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19745 Z= 0.252 Angle : 0.717 19.070 26894 Z= 0.375 Chirality : 0.045 0.269 3050 Planarity : 0.004 0.053 3212 Dihedral : 16.246 162.704 3392 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.04 % Favored : 90.78 % Rotamer: Outliers : 2.01 % Allowed : 15.02 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.17), residues: 2202 helix: 0.08 (0.18), residues: 843 sheet: -1.51 (0.26), residues: 350 loop : -2.45 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 58 TYR 0.017 0.002 TYR J 283 PHE 0.019 0.002 PHE D 129 TRP 0.010 0.002 TRP A 334 HIS 0.006 0.001 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00544 (19742) covalent geometry : angle 0.70029 (26888) SS BOND : bond 0.02524 ( 3) SS BOND : angle 10.20048 ( 6) hydrogen bonds : bond 0.04130 ( 733) hydrogen bonds : angle 5.43456 ( 2111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 MET cc_start: 0.8630 (mtp) cc_final: 0.8400 (ttt) REVERT: C 39 HIS cc_start: 0.7466 (m90) cc_final: 0.7260 (m-70) REVERT: A 142 PRO cc_start: 0.5092 (Cg_exo) cc_final: 0.4824 (Cg_endo) REVERT: A 580 MET cc_start: 0.8537 (mtm) cc_final: 0.8206 (ttm) outliers start: 39 outliers final: 26 residues processed: 114 average time/residue: 0.1167 time to fit residues: 22.4326 Evaluate side-chains 105 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 164 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN J 92 GLN ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.078745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.061007 restraints weight = 95557.634| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.59 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19745 Z= 0.259 Angle : 0.722 19.013 26894 Z= 0.378 Chirality : 0.045 0.271 3050 Planarity : 0.004 0.051 3212 Dihedral : 16.269 161.576 3392 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.36 % Favored : 90.46 % Rotamer: Outliers : 1.96 % Allowed : 15.80 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.17), residues: 2202 helix: 0.03 (0.18), residues: 843 sheet: -1.53 (0.26), residues: 354 loop : -2.47 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 70 TYR 0.018 0.002 TYR J 283 PHE 0.018 0.002 PHE G 96 TRP 0.011 0.002 TRP A 186 HIS 0.004 0.001 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00562 (19742) covalent geometry : angle 0.70558 (26888) SS BOND : bond 0.02547 ( 3) SS BOND : angle 10.22265 ( 6) hydrogen bonds : bond 0.04158 ( 733) hydrogen bonds : angle 5.48041 ( 2111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 MET cc_start: 0.8702 (mtp) cc_final: 0.8435 (ttt) REVERT: C 39 HIS cc_start: 0.7518 (m90) cc_final: 0.7014 (m90) REVERT: C 109 GLN cc_start: 0.8489 (mm-40) cc_final: 0.7722 (tm-30) REVERT: A 142 PRO cc_start: 0.5108 (Cg_exo) cc_final: 0.4843 (Cg_endo) outliers start: 38 outliers final: 32 residues processed: 119 average time/residue: 0.1124 time to fit residues: 22.8576 Evaluate side-chains 111 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 210 GLU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 87 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.078519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.060856 restraints weight = 95459.586| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.61 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 19745 Z= 0.262 Angle : 0.732 18.949 26894 Z= 0.382 Chirality : 0.045 0.273 3050 Planarity : 0.004 0.050 3212 Dihedral : 16.305 161.521 3392 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.63 % Favored : 90.19 % Rotamer: Outliers : 2.27 % Allowed : 16.06 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.17), residues: 2202 helix: 0.02 (0.18), residues: 844 sheet: -1.54 (0.26), residues: 342 loop : -2.49 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 70 TYR 0.019 0.002 TYR J 283 PHE 0.017 0.002 PHE F 162 TRP 0.011 0.002 TRP A 186 HIS 0.005 0.001 HIS J 155 Details of bonding type rmsd covalent geometry : bond 0.00568 (19742) covalent geometry : angle 0.71552 (26888) SS BOND : bond 0.02561 ( 3) SS BOND : angle 10.21688 ( 6) hydrogen bonds : bond 0.04213 ( 733) hydrogen bonds : angle 5.52593 ( 2111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: B 94 LYS cc_start: 0.8236 (pttm) cc_final: 0.7634 (mtpt) REVERT: G 53 MET cc_start: 0.8709 (mtp) cc_final: 0.8444 (ttt) REVERT: C 39 HIS cc_start: 0.7510 (m90) cc_final: 0.6967 (m90) REVERT: C 62 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: C 109 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7784 (tm-30) REVERT: A 142 PRO cc_start: 0.5092 (Cg_exo) cc_final: 0.4826 (Cg_endo) outliers start: 44 outliers final: 35 residues processed: 118 average time/residue: 0.1173 time to fit residues: 23.6306 Evaluate side-chains 114 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 74 optimal weight: 0.7980 chunk 123 optimal weight: 0.0060 chunk 121 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 216 optimal weight: 0.0770 chunk 138 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.082050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064528 restraints weight = 100615.743| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.88 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19745 Z= 0.116 Angle : 0.637 18.249 26894 Z= 0.328 Chirality : 0.042 0.194 3050 Planarity : 0.003 0.051 3212 Dihedral : 15.613 157.540 3392 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 1.60 % Allowed : 16.78 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2202 helix: 0.26 (0.18), residues: 855 sheet: -1.46 (0.26), residues: 344 loop : -2.34 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 70 TYR 0.015 0.001 TYR B 232 PHE 0.015 0.001 PHE C 129 TRP 0.009 0.001 TRP A 186 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00241 (19742) covalent geometry : angle 0.62024 (26888) SS BOND : bond 0.02314 ( 3) SS BOND : angle 9.76647 ( 6) hydrogen bonds : bond 0.03563 ( 733) hydrogen bonds : angle 5.08655 ( 2111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: H 53 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8236 (ttp) REVERT: C 39 HIS cc_start: 0.7717 (m90) cc_final: 0.7315 (m-70) REVERT: C 62 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: J 277 VAL cc_start: 0.8777 (t) cc_final: 0.8539 (m) outliers start: 31 outliers final: 22 residues processed: 125 average time/residue: 0.1110 time to fit residues: 23.5579 Evaluate side-chains 114 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 25 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 189 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 ASN A 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.081955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.064288 restraints weight = 94493.230| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 4.77 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19745 Z= 0.118 Angle : 0.629 18.217 26894 Z= 0.324 Chirality : 0.041 0.189 3050 Planarity : 0.003 0.038 3212 Dihedral : 15.602 160.645 3392 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.54 % Favored : 92.33 % Rotamer: Outliers : 1.29 % Allowed : 17.09 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.18), residues: 2202 helix: 0.37 (0.18), residues: 855 sheet: -1.46 (0.25), residues: 385 loop : -2.38 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 70 TYR 0.013 0.001 TYR F 55 PHE 0.013 0.001 PHE C 129 TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS J 282 Details of bonding type rmsd covalent geometry : bond 0.00251 (19742) covalent geometry : angle 0.61132 (26888) SS BOND : bond 0.02278 ( 3) SS BOND : angle 9.80542 ( 6) hydrogen bonds : bond 0.03495 ( 733) hydrogen bonds : angle 5.01544 ( 2111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: H 53 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8141 (ttp) REVERT: H 120 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: C 39 HIS cc_start: 0.7715 (m90) cc_final: 0.7323 (m-70) REVERT: C 62 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: J 277 VAL cc_start: 0.8735 (t) cc_final: 0.8496 (m) outliers start: 25 outliers final: 21 residues processed: 116 average time/residue: 0.1081 time to fit residues: 21.3399 Evaluate side-chains 112 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 195 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** J 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.080269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.063935 restraints weight = 119477.748| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.51 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19745 Z= 0.182 Angle : 0.668 18.564 26894 Z= 0.344 Chirality : 0.043 0.203 3050 Planarity : 0.004 0.066 3212 Dihedral : 15.776 161.424 3392 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.36 % Favored : 91.55 % Rotamer: Outliers : 1.39 % Allowed : 17.09 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.18), residues: 2202 helix: 0.39 (0.18), residues: 849 sheet: -1.40 (0.26), residues: 364 loop : -2.28 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.016 0.002 TYR A 74 PHE 0.015 0.001 PHE C 129 TRP 0.009 0.001 TRP A 334 HIS 0.005 0.001 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00395 (19742) covalent geometry : angle 0.65119 (26888) SS BOND : bond 0.02455 ( 3) SS BOND : angle 10.02613 ( 6) hydrogen bonds : bond 0.03701 ( 733) hydrogen bonds : angle 5.16347 ( 2111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3750.46 seconds wall clock time: 66 minutes 26.26 seconds (3986.26 seconds total)