Starting phenix.real_space_refine on Sun Sep 13 00:17:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xn4_22267/09_2026/6xn4_22267.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xn4_22267/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6xn4_22267/09_2026/6xn4_22267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xn4_22267/09_2026/6xn4_22267.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xn4_22267/09_2026/6xn4_22267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xn4_22267/09_2026/6xn4_22267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xn4_22267/09_2026/6xn4_22267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xn4_22267/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 35} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 16, 'rna3p': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: {'RNAv2': 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: 4.27, per 1000 atoms: 0.22 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: 1.61 Conformation dependent library (CDL) restraints added in 831.5 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: 2.12 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: 3.44 Time building geometry restraints manager: 2.14 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: 26414 4.07 - 8.15: 440 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: 11368 34.63 - 69.25: 386 69.25 - 103.88: 32 103.88 - 138.50: 1 138.50 - 173.13: 1 Dihedral angle restraints: 11788 sinusoidal: 5288 harmonic: 6500 Sorted by residual: dihedral pdb=" C4' A T 29 " pdb=" C3' A T 29 " pdb=" C2' A T 29 " pdb=" C1' A T 29 " ideal model delta sinusoidal sigma weight residual 36.35 -43.60 79.95 1 3.10e+00 1.04e-01 8.25e+02 dihedral pdb=" C4' C T 23 " pdb=" C3' C T 23 " pdb=" C2' C T 23 " pdb=" C1' C T 23 " ideal model delta sinusoidal sigma weight residual 36.34 -39.98 76.32 1 3.10e+00 1.04e-01 7.63e+02 dihedral pdb=" C4' C R 31 " pdb=" C3' C R 31 " pdb=" C2' C R 31 " pdb=" C1' C R 31 " ideal model delta sinusoidal sigma weight residual 36.34 -39.05 75.40 1 3.10e+00 1.04e-01 7.47e+02 ... (remaining 11785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2608 0.100 - 0.200: 330 0.200 - 0.300: 95 0.300 - 0.399: 14 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 2.46 2.03 0.43 2.00e-01 2.50e+01 4.58e+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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.180 Find NCS groups from input model: 0.180 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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= 0.407 Angle : 1.288 20.371 26894 Z= 0.684 Chirality : 0.080 0.499 3050 Planarity : 0.006 0.052 3212 Dihedral : 17.020 173.125 7595 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/Z covalent geometry : bond 0.00897 / 0.41 (19742) covalent geometry : angle 1.27977 / 0.68 (26888) SS BOND : bond 0.01710 / 0.84 ( 3) SS BOND : angle 9.81106 / 4.45 ( 6) hydrogen bonds : bond 0.19668 / 12.43 ( 733) hydrogen bonds : angle 8.48547 / 5.76 ( 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 : 0.873 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: 0.1272 time to fit residues: 22.6896 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 : 0.771 ------------------------------------------------------------------------------- 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... F 16 HIS H 124 ASN H 192 ASN G 121 ASN A 251 ASN A 355 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 = 0.4025 r_free = 0.4025 target = 0.081354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.064194 restraints weight = 86098.658| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 4.47 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 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 = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19745 Z= 0.185 Angle : 0.977 27.798 26894 Z= 0.456 Chirality : 0.085 1.378 3050 Planarity : 0.004 0.054 3212 Dihedral : 13.638 167.539 3194 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.23 % Rotamer: Outliers : 0.62 % Allowed : 6.97 % Favored : 92.41 % 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: -2.74 (0.16), residues: 2202 helix: -1.01 (0.16), residues: 848 sheet: -1.67 (0.24), residues: 375 loop : -2.58 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 311 TYR 0.018 0.002 TYR J 283 PHE 0.035 0.002 PHE A 36 TRP 0.009 0.002 TRP A 186 HIS 0.005 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (19742) covalent geometry : angle 0.96623 / 0.45 (26888) SS BOND : bond 0.01975 / 0.97 ( 3) SS BOND : angle 9.92191 / 4.54 ( 6) hydrogen bonds : bond 0.04563 / 2.91 ( 733) hydrogen bonds : angle 6.05115 / 4.18 ( 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 117 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.701 Fit side-chains REVERT: A 86 MET cc_start: 0.2179 (mpp) cc_final: 0.1605 (mpp) REVERT: A 250 MET cc_start: 0.8578 (tmm) cc_final: 0.8137 (tmm) REVERT: A 453 MET cc_start: 0.8227 (ttm) cc_final: 0.7934 (ttt) outliers start: 12 outliers final: 4 residues processed: 112 average time/residue: 0.1239 time to fit residues: 22.7947 Evaluate side-chains 88 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 208 ASN F 131 ASN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 HIS ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS J 63 ASN J 74 ASN J 282 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.078970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.062302 restraints weight = 119227.528| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.49 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 19745 Z= 0.285 Angle : 0.936 19.727 26894 Z= 0.452 Chirality : 0.077 1.218 3050 Planarity : 0.005 0.053 3212 Dihedral : 13.959 170.147 3194 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.42 % Rotamer: Outliers : 1.24 % Allowed : 11.46 % Favored : 87.30 % 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: -2.39 (0.17), residues: 2202 helix: -0.53 (0.17), residues: 842 sheet: -1.54 (0.25), residues: 360 loop : -2.54 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 719 TYR 0.036 0.002 TYR J 71 PHE 0.025 0.002 PHE A 36 TRP 0.018 0.002 TRP A 186 HIS 0.007 0.002 HIS J 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.28 (19742) covalent geometry : angle 0.92368 / 0.45 (26888) SS BOND : bond 0.02390 / 1.17 ( 3) SS BOND : angle 10.33301 / 4.84 ( 6) hydrogen bonds : bond 0.04563 / 2.87 ( 733) hydrogen bonds : angle 5.85530 / 4.07 ( 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 113 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.630 Fit side-chains REVERT: G 53 MET cc_start: 0.8707 (mtp) cc_final: 0.8394 (ttt) REVERT: A 86 MET cc_start: 0.2606 (mpp) cc_final: 0.2137 (mpp) REVERT: A 250 MET cc_start: 0.8524 (tmm) cc_final: 0.8234 (tmm) outliers start: 24 outliers final: 7 residues processed: 105 average time/residue: 0.1116 time to fit residues: 20.1000 Evaluate side-chains 86 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 211 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.082381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064489 restraints weight = 114251.541| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 5.30 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 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 = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19745 Z= 0.136 Angle : 0.770 18.775 26894 Z= 0.371 Chirality : 0.061 0.827 3050 Planarity : 0.004 0.055 3212 Dihedral : 13.749 176.427 3194 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 1.50 % Allowed : 12.65 % Favored : 85.85 % 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: -2.07 (0.17), residues: 2202 helix: -0.15 (0.18), residues: 851 sheet: -1.50 (0.25), residues: 375 loop : -2.44 (0.18), residues: 976 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 0.018 0.001 PHE A 36 TRP 0.017 0.001 TRP A 186 HIS 0.004 0.001 HIS J 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (19742) covalent geometry : angle 0.75587 / 0.36 (26888) SS BOND : bond 0.02228 / 1.10 ( 3) SS BOND : angle 9.82096 / 4.59 ( 6) hydrogen bonds : bond 0.03741 / 2.39 ( 733) hydrogen bonds : angle 5.29576 / 3.71 ( 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 131 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: C 109 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7604 (tm-30) REVERT: A 86 MET cc_start: 0.1771 (mpp) cc_final: 0.1455 (mtt) REVERT: A 250 MET cc_start: 0.8527 (tmm) cc_final: 0.8185 (tmm) REVERT: J 277 VAL cc_start: 0.8724 (t) cc_final: 0.8509 (m) outliers start: 29 outliers final: 13 residues processed: 123 average time/residue: 0.1287 time to fit residues: 26.4496 Evaluate side-chains 99 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET 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 195 VAL 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 C residue 62 GLU Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 302 ILE 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: 10.0000 chunk 94 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 105 optimal weight: 0.0070 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: 0.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4055 r_free = 0.4055 target = 0.082584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.065251 restraints weight = 101029.127| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 4.68 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 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 = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2691 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= 0.131 Angle : 0.737 18.512 26894 Z= 0.355 Chirality : 0.059 0.642 3050 Planarity : 0.003 0.057 3212 Dihedral : 13.494 174.688 3194 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 1.50 % Allowed : 14.61 % Favored : 83.89 % 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: -1.86 (0.17), residues: 2202 helix: 0.09 (0.18), residues: 855 sheet: -1.32 (0.26), residues: 369 loop : -2.43 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 134 TYR 0.015 0.001 TYR A 77 PHE 0.015 0.001 PHE A 36 TRP 0.012 0.001 TRP A 186 HIS 0.003 0.001 HIS J 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (19742) covalent geometry : angle 0.72284 / 0.35 (26888) SS BOND : bond 0.02223 / 1.09 ( 3) SS BOND : angle 9.76706 / 4.58 ( 6) hydrogen bonds : bond 0.03610 / 2.30 ( 733) hydrogen bonds : angle 5.13366 / 3.59 ( 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 131 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6199 (mm) REVERT: C 39 HIS cc_start: 0.7678 (m90) cc_final: 0.7455 (m-70) REVERT: C 109 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7615 (tm-30) REVERT: A 75 ILE cc_start: 0.8123 (mm) cc_final: 0.7918 (mp) REVERT: A 142 PRO cc_start: 0.4899 (Cg_exo) cc_final: 0.4635 (Cg_endo) REVERT: A 250 MET cc_start: 0.8703 (tmm) cc_final: 0.8267 (tmm) REVERT: J 277 VAL cc_start: 0.8811 (t) cc_final: 0.8579 (m) outliers start: 29 outliers final: 17 residues processed: 123 average time/residue: 0.1338 time to fit residues: 27.1956 Evaluate side-chains 112 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET 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 A residue 302 ILE 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: 0.9980 chunk 153 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 0.0270 chunk 219 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.080859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.063312 restraints weight = 93619.092| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.56 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 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 = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19745 Z= 0.190 Angle : 0.780 18.724 26894 Z= 0.375 Chirality : 0.062 0.752 3050 Planarity : 0.004 0.052 3212 Dihedral : 13.670 178.628 3194 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.33 % Rotamer: Outliers : 1.91 % Allowed : 15.18 % Favored : 82.91 % 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: -1.79 (0.17), residues: 2202 helix: 0.22 (0.18), residues: 847 sheet: -1.40 (0.25), residues: 370 loop : -2.39 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 719 TYR 0.015 0.002 TYR F 55 PHE 0.018 0.001 PHE C 129 TRP 0.009 0.001 TRP A 334 HIS 0.004 0.001 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (19742) covalent geometry : angle 0.76521 / 0.37 (26888) SS BOND : bond 0.02384 / 1.17 ( 3) SS BOND : angle 9.99122 / 4.72 ( 6) hydrogen bonds : bond 0.03753 / 2.36 ( 733) hydrogen bonds : angle 5.21597 / 3.65 ( 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 132 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 53 MET cc_start: 0.8598 (mtp) cc_final: 0.8383 (ttt) REVERT: G 208 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6083 (mm) REVERT: C 39 HIS cc_start: 0.7545 (m90) cc_final: 0.7325 (m90) REVERT: C 109 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7684 (tm-30) REVERT: A 75 ILE cc_start: 0.8272 (mm) cc_final: 0.7735 (mt) REVERT: A 142 PRO cc_start: 0.5071 (Cg_exo) cc_final: 0.4811 (Cg_endo) REVERT: A 250 MET cc_start: 0.8540 (tmm) cc_final: 0.8103 (tmm) REVERT: J 277 VAL cc_start: 0.8717 (t) cc_final: 0.8497 (m) outliers start: 37 outliers final: 26 residues processed: 125 average time/residue: 0.1263 time to fit residues: 26.5904 Evaluate side-chains 118 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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 D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS 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 580 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 164 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 222 optimal weight: 0.0970 chunk 37 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.080449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.062939 restraints weight = 94965.603| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 4.82 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 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 = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2749 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= 0.196 Angle : 0.790 18.771 26894 Z= 0.380 Chirality : 0.063 0.789 3050 Planarity : 0.004 0.049 3212 Dihedral : 13.715 178.039 3194 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.33 % Rotamer: Outliers : 1.76 % Allowed : 15.95 % Favored : 82.29 % 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: -1.76 (0.17), residues: 2202 helix: 0.23 (0.18), residues: 851 sheet: -1.36 (0.25), residues: 364 loop : -2.38 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 70 TYR 0.015 0.002 TYR H 55 PHE 0.016 0.001 PHE C 129 TRP 0.008 0.001 TRP A 334 HIS 0.004 0.001 HIS J 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (19742) covalent geometry : angle 0.77545 / 0.37 (26888) SS BOND : bond 0.02410 / 1.18 ( 3) SS BOND : angle 10.02625 / 4.74 ( 6) hydrogen bonds : bond 0.03790 / 2.38 ( 733) hydrogen bonds : angle 5.24927 / 3.68 ( 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 128 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8864 (p) REVERT: G 208 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6211 (mm) REVERT: C 39 HIS cc_start: 0.7611 (m90) cc_final: 0.7349 (m90) REVERT: C 109 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7724 (tm-30) REVERT: A 142 PRO cc_start: 0.5289 (Cg_exo) cc_final: 0.5039 (Cg_endo) REVERT: A 250 MET cc_start: 0.8652 (tmm) cc_final: 0.8130 (tmm) REVERT: J 277 VAL cc_start: 0.8725 (t) cc_final: 0.8502 (m) outliers start: 34 outliers final: 27 residues processed: 122 average time/residue: 0.1231 time to fit residues: 25.3967 Evaluate side-chains 119 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 C residue 130 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain A residue 8 CYS 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 580 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: 9.9990 chunk 224 optimal weight: 0.0000 chunk 91 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.081348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.063966 restraints weight = 94836.735| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 4.82 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 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 = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.004 0.050 19745 Z= 0.161 Angle : 0.759 18.492 26894 Z= 0.365 Chirality : 0.061 0.746 3050 Planarity : 0.003 0.049 3212 Dihedral : 13.611 176.142 3194 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.78 % Rotamer: Outliers : 1.81 % Allowed : 16.16 % Favored : 82.03 % 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: -1.71 (0.17), residues: 2202 helix: 0.26 (0.18), residues: 856 sheet: -1.38 (0.25), residues: 368 loop : -2.34 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 70 TYR 0.014 0.001 TYR H 55 PHE 0.016 0.001 PHE C 129 TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS J 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (19742) covalent geometry : angle 0.74470 / 0.36 (26888) SS BOND : bond 0.02364 / 1.16 ( 3) SS BOND : angle 9.91883 / 4.69 ( 6) hydrogen bonds : bond 0.03633 / 2.29 ( 733) hydrogen bonds : angle 5.16091 / 3.62 ( 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 129 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6326 (ptt) REVERT: H 121 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.6576 (p0) REVERT: G 208 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6203 (mm) REVERT: C 39 HIS cc_start: 0.7665 (m90) cc_final: 0.7031 (m90) REVERT: C 109 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7721 (tm-30) REVERT: A 142 PRO cc_start: 0.5297 (Cg_exo) cc_final: 0.5041 (Cg_endo) REVERT: A 250 MET cc_start: 0.8664 (tmm) cc_final: 0.8173 (tmm) REVERT: A 553 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: J 277 VAL cc_start: 0.8734 (t) cc_final: 0.8494 (m) outliers start: 35 outliers final: 27 residues processed: 123 average time/residue: 0.1275 time to fit residues: 26.2347 Evaluate side-chains 120 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 76 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 29 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 52 LYS Chi-restraints excluded: chain H residue 121 ASN 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 C residue 84 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 103 VAL 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 553 PHE Chi-restraints excluded: chain A residue 580 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 216 optimal weight: 0.0020 chunk 138 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 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 = 0.4047 r_free = 0.4047 target = 0.082395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.064832 restraints weight = 100817.768| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 4.97 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 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 = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19745 Z= 0.133 Angle : 0.733 18.344 26894 Z= 0.352 Chirality : 0.058 0.679 3050 Planarity : 0.003 0.048 3212 Dihedral : 13.483 175.413 3194 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.58 % Favored : 92.33 % Rotamer: Outliers : 1.86 % Allowed : 16.26 % Favored : 81.88 % 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: -1.63 (0.17), residues: 2202 helix: 0.37 (0.18), residues: 861 sheet: -1.35 (0.25), residues: 368 loop : -2.34 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.014 0.001 TYR H 55 PHE 0.015 0.001 PHE C 129 TRP 0.010 0.001 TRP A 186 HIS 0.004 0.001 HIS J 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19742) covalent geometry : angle 0.71872 / 0.35 (26888) SS BOND : bond 0.02285 / 1.12 ( 3) SS BOND : angle 9.81946 / 4.64 ( 6) hydrogen bonds : bond 0.03479 / 2.20 ( 733) hydrogen bonds : angle 5.02975 / 3.53 ( 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 128 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6242 (ptt) REVERT: H 53 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: H 121 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.6710 (p0) REVERT: G 53 MET cc_start: 0.8382 (mtp) cc_final: 0.8110 (ttt) REVERT: G 208 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6061 (mm) REVERT: C 39 HIS cc_start: 0.7758 (m90) cc_final: 0.7266 (m-70) REVERT: C 62 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: C 106 ASP cc_start: 0.7568 (p0) cc_final: 0.7360 (p0) REVERT: C 109 GLN cc_start: 0.8460 (mm-40) cc_final: 0.7711 (tm-30) REVERT: A 142 PRO cc_start: 0.5214 (Cg_exo) cc_final: 0.4959 (Cg_endo) REVERT: A 250 MET cc_start: 0.8656 (tmm) cc_final: 0.8187 (tmm) REVERT: A 553 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: J 277 VAL cc_start: 0.8757 (t) cc_final: 0.8532 (m) outliers start: 36 outliers final: 24 residues processed: 121 average time/residue: 0.1271 time to fit residues: 26.1374 Evaluate side-chains 120 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 76 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 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 121 ASN 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 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 C residue 130 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 VAL 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 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain J residue 84 VAL 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: 9.9990 chunk 79 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.079486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.062140 restraints weight = 95330.587| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 4.65 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19745 Z= 0.272 Angle : 0.856 18.874 26894 Z= 0.412 Chirality : 0.066 0.841 3050 Planarity : 0.004 0.049 3212 Dihedral : 13.894 179.896 3194 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.22 % Favored : 90.64 % Rotamer: Outliers : 1.70 % Allowed : 16.57 % Favored : 81.72 % 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: -1.72 (0.17), residues: 2202 helix: 0.27 (0.18), residues: 847 sheet: -1.29 (0.26), residues: 352 loop : -2.36 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 70 TYR 0.019 0.002 TYR B 186 PHE 0.018 0.002 PHE D 129 TRP 0.010 0.002 TRP A 186 HIS 0.007 0.001 HIS J 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 (19742) covalent geometry : angle 0.84273 / 0.41 (26888) SS BOND : bond 0.02474 / 1.21 ( 3) SS BOND : angle 10.14190 / 4.81 ( 6) hydrogen bonds : bond 0.04056 / 2.54 ( 733) hydrogen bonds : angle 5.38626 / 3.77 ( 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 126 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 121 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.6797 (p0) REVERT: G 53 MET cc_start: 0.8537 (mtp) cc_final: 0.8235 (ttt) REVERT: G 208 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6327 (mm) REVERT: C 39 HIS cc_start: 0.7637 (m90) cc_final: 0.7072 (m90) REVERT: C 109 GLN cc_start: 0.8576 (mm-40) cc_final: 0.7898 (tm-30) REVERT: A 142 PRO cc_start: 0.5357 (Cg_exo) cc_final: 0.5149 (Cg_endo) REVERT: A 250 MET cc_start: 0.8696 (tmm) cc_final: 0.8168 (tmm) REVERT: A 553 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8008 (m-10) outliers start: 33 outliers final: 27 residues processed: 119 average time/residue: 0.1256 time to fit residues: 25.3725 Evaluate side-chains 118 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 121 ASN 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 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 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 103 VAL 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 553 PHE Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain J residue 84 VAL 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: 6.9990 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.081156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.064650 restraints weight = 119799.776| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 4.77 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 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 = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19745 Z= 0.165 Angle : 0.771 18.550 26894 Z= 0.370 Chirality : 0.061 0.767 3050 Planarity : 0.003 0.048 3212 Dihedral : 13.710 176.514 3194 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.99 % Favored : 91.92 % Rotamer: Outliers : 1.76 % Allowed : 16.68 % Favored : 81.57 % 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: -1.61 (0.18), residues: 2202 helix: 0.39 (0.18), residues: 844 sheet: -1.33 (0.26), residues: 350 loop : -2.28 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.013 0.001 TYR B 287 PHE 0.017 0.001 PHE C 129 TRP 0.009 0.001 TRP A 186 HIS 0.005 0.001 HIS J 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (19742) covalent geometry : angle 0.75688 / 0.36 (26888) SS BOND : bond 0.02380 / 1.17 ( 3) SS BOND : angle 9.92930 / 4.70 ( 6) hydrogen bonds : bond 0.03681 / 2.31 ( 733) hydrogen bonds : angle 5.20428 / 3.66 ( 2111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4223.64 seconds wall clock time: 73 minutes 53.18 seconds (4433.18 seconds total)