Starting phenix.real_space_refine on Sat Sep 12 18:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xn5_22268/09_2026/6xn5_22268.cif" } resolution = 2.97 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= 0.013 sd= 1.147 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 31 5.49 5 S 47 5.16 5 C 10948 2.51 5 N 2946 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 17400 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" 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: "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: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1629 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 5939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5939 Classifications: {'peptide': 735} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 723} Chain breaks: 3 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: "B" Number of atoms: 2278 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} 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: 282, 2276 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} 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: 2323 Chain: "G" 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: "J" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1917 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 227} Chain breaks: 3 Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 674 Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 17, 'rna3p': 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.23 Number of scatterers: 17400 At special positions: 0 Unit cell: (122.436, 126.732, 205.134, 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 47 16.00 P 31 15.00 O 3428 8.00 N 2946 7.00 C 10948 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=2.00 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.07 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.02 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: 1.47 Conformation dependent library (CDL) restraints added in 817.1 milliseconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 27 sheets defined 37.5% alpha, 16.4% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 74 through 81 Processing helix chain 'I' and resid 103 through 109 removed outlier: 3.700A pdb=" N LEU I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 173 Processing helix chain 'I' and resid 204 through 213 removed outlier: 4.285A pdb=" N LEU I 208 " --> pdb=" O LYS I 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 103 through 110 removed outlier: 3.910A pdb=" N PHE F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) 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 174 Processing helix chain 'F' and resid 205 through 213 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 110 removed outlier: 3.614A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 157 through 173 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.596A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.636A 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 202 through 224 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.953A pdb=" N GLU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 268 through 271 removed outlier: 3.531A pdb=" N LYS A 271 " --> pdb=" O LYS A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 272 through 295 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 317 through 339 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 363 through 381 removed outlier: 4.178A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.581A pdb=" N ASP A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 463 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.720A pdb=" N VAL A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.745A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.298A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.518A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 Processing helix chain 'A' and resid 686 through 704 removed outlier: 3.919A pdb=" N ALA A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 725 removed outlier: 3.678A pdb=" N ILE A 710 " --> pdb=" O GLN A 706 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.537A pdb=" N ASN B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.770A pdb=" N TYR B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.681A pdb=" N ALA B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.501A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 154 through 174 removed outlier: 3.527A pdb=" N VAL G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS G 160 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 212 Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.124A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 227 removed outlier: 3.897A pdb=" N ASN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 235 removed outlier: 3.570A pdb=" N GLY J 232 " --> pdb=" O TRP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 300 Processing sheet with id=AA1, first strand: chain 'I' and resid 188 through 191 removed outlier: 3.750A pdb=" N ILE I 196 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 188 through 191 removed outlier: 6.271A pdb=" N GLU I 147 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN I 97 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY H 184 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE I 96 " --> pdb=" O GLY H 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'I' and resid 115 through 119 Processing sheet with id=AA5, first strand: chain 'F' and resid 188 through 199 removed outlier: 5.286A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU F 147 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN F 97 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY B 185 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE F 96 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.119A pdb=" N ASN G 97 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU G 147 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 143 through 151 removed outlier: 4.718A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 97 removed outlier: 6.715A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 120 Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.497A pdb=" N LEU A 107 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.730A pdb=" N TYR A 311 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 305 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.730A pdb=" N TYR A 311 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 305 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 350 " --> pdb=" O MET A 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.700A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.482A pdb=" N PHE A 579 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 653 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AC3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AC4, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.505A pdb=" N LEU B 256 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.592A pdb=" N ASP B 272 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC8, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.073A pdb=" N VAL J 158 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER J 202 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP J 160 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR J 200 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR J 8 " --> pdb=" O LYS J 348 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS J 348 " --> pdb=" O THR J 8 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR J 10 " --> pdb=" O ARG J 346 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG J 346 " --> pdb=" O THR J 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA J 345 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE J 268 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 169 through 172 removed outlier: 3.932A pdb=" N LYS J 170 " --> pdb=" O CYS J 190 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS J 190 " --> pdb=" O LYS J 170 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR J 172 " --> pdb=" O ARG J 188 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG J 188 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 690 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.94 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: 5533 1.34 - 1.46: 4258 1.46 - 1.59: 7833 1.59 - 1.72: 42 1.72 - 1.84: 87 Bond restraints: 17753 Sorted by residual: bond pdb=" CA GLU A 704 " pdb=" C GLU A 704 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.80e-02 3.09e+03 8.24e+00 bond pdb=" CB PRO I 70 " pdb=" CG PRO I 70 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N PRO I 70 " pdb=" CD PRO I 70 " ideal model delta sigma weight residual 1.473 1.504 -0.031 1.40e-02 5.10e+03 4.80e+00 bond pdb=" CG1 ILE G 139 " pdb=" CD1 ILE G 139 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.62e+00 bond pdb=" N ASP J 112 " pdb=" CA ASP J 112 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.93e+00 ... (remaining 17748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 23405 3.16 - 6.32: 556 6.32 - 9.48: 66 9.48 - 12.64: 10 12.64 - 15.80: 3 Bond angle restraints: 24040 Sorted by residual: angle pdb=" CA PRO I 70 " pdb=" N PRO I 70 " pdb=" CD PRO I 70 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.24e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 106.06 7.65 9.50e-01 1.11e+00 6.49e+01 angle pdb=" C LYS A 683 " pdb=" N LEU A 684 " pdb=" CA LEU A 684 " ideal model delta sigma weight residual 121.70 133.14 -11.44 1.80e+00 3.09e-01 4.04e+01 angle pdb=" N VAL J 277 " pdb=" CA VAL J 277 " pdb=" C VAL J 277 " ideal model delta sigma weight residual 112.96 107.06 5.90 1.00e+00 1.00e+00 3.48e+01 angle pdb=" CA CYS A 405 " pdb=" CB CYS A 405 " pdb=" SG CYS A 405 " ideal model delta sigma weight residual 114.40 125.57 -11.17 2.30e+00 1.89e-01 2.36e+01 ... (remaining 24035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 9350 17.73 - 35.46: 1053 35.46 - 53.19: 180 53.19 - 70.92: 72 70.92 - 88.65: 22 Dihedral angle restraints: 10677 sinusoidal: 4604 harmonic: 6073 Sorted by residual: dihedral pdb=" C4' G R 20 " pdb=" C3' G R 20 " pdb=" C2' G R 20 " pdb=" C1' G R 20 " ideal model delta sinusoidal sigma weight residual 36.35 -37.38 73.72 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' G R 3 " pdb=" C3' G R 3 " pdb=" C2' G R 3 " pdb=" C1' G R 3 " ideal model delta sinusoidal sigma weight residual 36.34 -36.97 73.32 1 3.10e+00 1.04e-01 7.12e+02 dihedral pdb=" C4' A R 1 " pdb=" C3' A R 1 " pdb=" C2' A R 1 " pdb=" C1' A R 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.56 72.90 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 10674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2127 0.073 - 0.145: 435 0.145 - 0.218: 89 0.218 - 0.291: 43 0.291 - 0.363: 14 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CG LEU H 78 " pdb=" CB LEU H 78 " pdb=" CD1 LEU H 78 " pdb=" CD2 LEU H 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" P G R 3 " pdb=" OP1 G R 3 " pdb=" OP2 G R 3 " pdb=" O5' G R 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.86e+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 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 2705 not shown) Planarity restraints: 2983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 553 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C PHE A 553 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE A 553 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS A 554 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 69 " 0.066 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO I 70 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO I 70 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 70 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 667 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLU A 667 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 667 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 668 " 0.019 2.00e-02 2.50e+03 ... (remaining 2980 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2228 2.75 - 3.29: 16154 3.29 - 3.82: 29425 3.82 - 4.36: 34951 4.36 - 4.90: 60835 Nonbonded interactions: 143593 Sorted by model distance: nonbonded pdb=" O MET B 76 " pdb=" OG SER B 231 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 202 " pdb=" OD2 ASP A 205 " model vdw 2.258 3.040 nonbonded pdb=" NH1 ARG H 54 " pdb=" OP1 U R 19 " model vdw 2.260 3.120 nonbonded pdb=" O ALA J 291 " pdb=" OG SER J 295 " model vdw 2.282 3.040 nonbonded pdb=" O ALA J 134 " pdb=" OG1 THR J 137 " model vdw 2.285 3.040 ... (remaining 143588 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 'F' and (resid 1 through 20 or resid 27 through 214)) selection = (chain 'G' and (resid 1 through 20 or resid 27 through 65 or resid 73 through 21 \ 4)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 20 or resid 27 through 65 or resid 73 through 21 \ 4)) } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.700 Find NCS groups from input model: 0.210 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.007 0.132 17756 Z= 0.322 Angle : 1.175 24.565 24046 Z= 0.621 Chirality : 0.072 0.363 2708 Planarity : 0.006 0.092 2983 Dihedral : 15.910 88.655 6760 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.06 % Allowed : 0.88 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.03 (0.16), residues: 2065 helix: -1.97 (0.15), residues: 738 sheet: -1.13 (0.26), residues: 357 loop : -2.32 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 365 TYR 0.041 0.003 TYR A 229 PHE 0.038 0.003 PHE J 296 TRP 0.009 0.003 TRP A 334 HIS 0.007 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.32 (17753) covalent geometry : angle 1.15114 / 0.61 (24040) SS BOND : bond 0.03150 / 1.57 ( 3) SS BOND : angle 14.98727 / 6.00 ( 6) hydrogen bonds : bond 0.16689 / 10.34 ( 679) hydrogen bonds : angle 8.52868 / 5.81 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.689 Fit side-chains REVERT: G 59 LYS cc_start: 0.7049 (tptp) cc_final: 0.6824 (tptt) outliers start: 1 outliers final: 4 residues processed: 235 average time/residue: 0.5679 time to fit residues: 151.2556 Evaluate side-chains 153 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain G residue 75 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN A 45 ASN A 147 ASN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN B 132 GLN G 180 HIS ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.143996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110916 restraints weight = 34876.248| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.58 r_work: 0.3345 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17756 Z= 0.147 Angle : 0.833 14.412 24046 Z= 0.396 Chirality : 0.073 1.047 2708 Planarity : 0.004 0.053 2983 Dihedral : 10.825 148.493 2652 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.27 % Allowed : 10.01 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.97 (0.17), residues: 2065 helix: -0.56 (0.18), residues: 746 sheet: -0.93 (0.26), residues: 364 loop : -2.04 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 18 TYR 0.019 0.001 TYR H 55 PHE 0.028 0.001 PHE J 296 TRP 0.005 0.001 TRP J 228 HIS 0.004 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (17753) covalent geometry : angle 0.82570 / 0.39 (24040) SS BOND : bond 0.01662 / 0.82 ( 3) SS BOND : angle 7.24787 / 2.88 ( 6) hydrogen bonds : bond 0.04113 / 2.73 ( 679) hydrogen bonds : angle 5.93547 / 4.03 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 174 PHE cc_start: 0.7982 (m-10) cc_final: 0.7584 (m-80) REVERT: I 175 ASP cc_start: 0.7890 (t0) cc_final: 0.7621 (t0) REVERT: F 108 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7349 (mm-30) REVERT: H 153 ASP cc_start: 0.6329 (t0) cc_final: 0.6087 (OUTLIER) REVERT: H 154 ASP cc_start: 0.6592 (m-30) cc_final: 0.6116 (m-30) REVERT: A 520 ASP cc_start: 0.8603 (p0) cc_final: 0.8399 (p0) REVERT: A 712 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7903 (ttm110) REVERT: B 244 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: G 59 LYS cc_start: 0.7702 (tptp) cc_final: 0.7188 (tptt) REVERT: J 310 MET cc_start: 0.3143 (OUTLIER) cc_final: 0.2889 (mtm) outliers start: 23 outliers final: 10 residues processed: 201 average time/residue: 0.5195 time to fit residues: 119.7105 Evaluate side-chains 163 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 148 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 180 HIS A 45 ASN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 425 GLN A 483 GLN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102321 restraints weight = 44789.493| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.09 r_work: 0.3190 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 17756 Z= 0.297 Angle : 0.891 17.395 24046 Z= 0.432 Chirality : 0.072 1.079 2708 Planarity : 0.004 0.041 2983 Dihedral : 11.371 146.039 2645 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.32 % Allowed : 13.00 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.82 (0.17), residues: 2065 helix: -0.25 (0.18), residues: 750 sheet: -0.99 (0.26), residues: 366 loop : -2.08 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 133 TYR 0.023 0.002 TYR H 55 PHE 0.028 0.002 PHE J 296 TRP 0.007 0.001 TRP A 186 HIS 0.005 0.001 HIS F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (17753) covalent geometry : angle 0.88101 / 0.43 (24040) SS BOND : bond 0.02155 / 1.06 ( 3) SS BOND : angle 8.39378 / 3.48 ( 6) hydrogen bonds : bond 0.04753 / 3.19 ( 679) hydrogen bonds : angle 5.90193 / 4.03 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 74 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6470 (mp10) REVERT: H 147 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: H 153 ASP cc_start: 0.6717 (t0) cc_final: 0.6363 (OUTLIER) REVERT: H 154 ASP cc_start: 0.6640 (m-30) cc_final: 0.5983 (m-30) REVERT: A 90 LYS cc_start: 0.9027 (mmmm) cc_final: 0.8794 (mmmm) REVERT: A 669 ASP cc_start: 0.7747 (m-30) cc_final: 0.7542 (m-30) REVERT: A 712 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7823 (ttm110) REVERT: B 244 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: G 59 LYS cc_start: 0.8032 (tptp) cc_final: 0.7476 (tptt) REVERT: J 157 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6692 (mt0) REVERT: J 310 MET cc_start: 0.3437 (OUTLIER) cc_final: 0.3146 (mtm) outliers start: 60 outliers final: 28 residues processed: 207 average time/residue: 0.5483 time to fit residues: 129.7174 Evaluate side-chains 179 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 22 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.142244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108188 restraints weight = 45372.929| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.95 r_work: 0.3292 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17756 Z= 0.128 Angle : 0.694 11.837 24046 Z= 0.339 Chirality : 0.057 0.712 2708 Planarity : 0.004 0.049 2983 Dihedral : 11.341 144.330 2645 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.77 % Allowed : 15.60 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.38 (0.18), residues: 2065 helix: 0.27 (0.19), residues: 752 sheet: -0.93 (0.26), residues: 370 loop : -1.89 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 18 TYR 0.019 0.001 TYR J 5 PHE 0.027 0.001 PHE J 296 TRP 0.005 0.001 TRP J 228 HIS 0.002 0.000 HIS H 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (17753) covalent geometry : angle 0.68478 / 0.33 (24040) SS BOND : bond 0.01330 / 0.65 ( 3) SS BOND : angle 7.34992 / 3.04 ( 6) hydrogen bonds : bond 0.03636 / 2.44 ( 679) hydrogen bonds : angle 5.34800 / 3.67 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: F 101 LEU cc_start: 0.9301 (tp) cc_final: 0.9097 (tp) REVERT: H 151 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8093 (p0) REVERT: H 153 ASP cc_start: 0.6756 (t0) cc_final: 0.6324 (t0) REVERT: H 154 ASP cc_start: 0.6604 (m-30) cc_final: 0.5973 (m-30) REVERT: A 90 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8772 (mmmm) REVERT: A 181 MET cc_start: 0.8871 (tmm) cc_final: 0.8650 (ttt) REVERT: A 503 MET cc_start: 0.8660 (ttp) cc_final: 0.8241 (ttt) REVERT: A 669 ASP cc_start: 0.7731 (m-30) cc_final: 0.7523 (m-30) REVERT: A 712 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7887 (ttm110) REVERT: B 50 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8058 (mm-40) REVERT: B 152 ASN cc_start: 0.7907 (t0) cc_final: 0.7681 (t0) REVERT: B 244 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: G 59 LYS cc_start: 0.7797 (tptp) cc_final: 0.7167 (tptt) REVERT: G 151 ASN cc_start: 0.8614 (p0) cc_final: 0.8037 (t0) REVERT: J 157 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6324 (mt0) REVERT: J 206 GLU cc_start: 0.1982 (OUTLIER) cc_final: 0.0778 (tt0) REVERT: J 310 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2933 (mtm) outliers start: 50 outliers final: 18 residues processed: 204 average time/residue: 0.5396 time to fit residues: 125.7703 Evaluate side-chains 184 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 204 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 199 optimal weight: 0.0050 chunk 12 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 180 HIS A 45 ASN A 530 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.139864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106798 restraints weight = 42491.705| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.99 r_work: 0.3250 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17756 Z= 0.183 Angle : 0.728 12.227 24046 Z= 0.354 Chirality : 0.059 0.814 2708 Planarity : 0.004 0.057 2983 Dihedral : 11.341 142.068 2645 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.48 % Allowed : 16.65 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.27 (0.18), residues: 2065 helix: 0.37 (0.19), residues: 755 sheet: -0.83 (0.26), residues: 360 loop : -1.85 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 125 TYR 0.022 0.001 TYR H 55 PHE 0.026 0.001 PHE J 296 TRP 0.004 0.001 TRP A 186 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (17753) covalent geometry : angle 0.71748 / 0.35 (24040) SS BOND : bond 0.01635 / 0.80 ( 3) SS BOND : angle 7.65556 / 3.19 ( 6) hydrogen bonds : bond 0.03861 / 2.59 ( 679) hydrogen bonds : angle 5.33175 / 3.67 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: F 101 LEU cc_start: 0.9329 (tp) cc_final: 0.9125 (tp) REVERT: F 171 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8540 (mp) REVERT: H 151 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8147 (p0) REVERT: H 153 ASP cc_start: 0.6874 (t0) cc_final: 0.6441 (t0) REVERT: H 154 ASP cc_start: 0.6671 (m-30) cc_final: 0.6086 (m-30) REVERT: A 90 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8820 (mmmm) REVERT: A 356 ASP cc_start: 0.7971 (t0) cc_final: 0.7622 (t0) REVERT: A 502 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 503 MET cc_start: 0.8730 (ttp) cc_final: 0.8443 (ttt) REVERT: A 669 ASP cc_start: 0.7728 (m-30) cc_final: 0.7509 (m-30) REVERT: A 712 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7898 (ttm110) REVERT: B 152 ASN cc_start: 0.7991 (t0) cc_final: 0.7773 (t0) REVERT: B 244 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: G 59 LYS cc_start: 0.7936 (tptp) cc_final: 0.7371 (tptt) REVERT: G 123 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7145 (pt) REVERT: J 206 GLU cc_start: 0.1814 (OUTLIER) cc_final: 0.0797 (tt0) outliers start: 63 outliers final: 28 residues processed: 211 average time/residue: 0.4811 time to fit residues: 117.5234 Evaluate side-chains 177 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 146 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 72 ASN A 45 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106460 restraints weight = 34669.241| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.55 r_work: 0.3274 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17756 Z= 0.180 Angle : 0.720 12.208 24046 Z= 0.351 Chirality : 0.058 0.816 2708 Planarity : 0.004 0.042 2983 Dihedral : 11.409 142.150 2645 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.76 % Allowed : 17.53 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.19 (0.18), residues: 2065 helix: 0.42 (0.19), residues: 754 sheet: -0.82 (0.26), residues: 364 loop : -1.79 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 125 TYR 0.023 0.001 TYR H 55 PHE 0.029 0.002 PHE J 296 TRP 0.004 0.001 TRP A 186 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (17753) covalent geometry : angle 0.70990 / 0.35 (24040) SS BOND : bond 0.01562 / 0.77 ( 3) SS BOND : angle 7.63759 / 3.19 ( 6) hydrogen bonds : bond 0.03804 / 2.55 ( 679) hydrogen bonds : angle 5.26843 / 3.63 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 101 LEU cc_start: 0.9307 (tp) cc_final: 0.9094 (tp) REVERT: F 136 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: F 171 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8494 (mp) REVERT: H 147 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: H 151 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8102 (p0) REVERT: H 153 ASP cc_start: 0.6898 (t0) cc_final: 0.6561 (t0) REVERT: A 181 MET cc_start: 0.8874 (tmm) cc_final: 0.8627 (ttt) REVERT: A 249 MET cc_start: 0.8900 (tpp) cc_final: 0.8675 (tpt) REVERT: A 356 ASP cc_start: 0.7950 (t0) cc_final: 0.7598 (t0) REVERT: A 447 MET cc_start: 0.8249 (ttm) cc_final: 0.7806 (mtp) REVERT: A 486 MET cc_start: 0.8606 (ptp) cc_final: 0.8383 (ptp) REVERT: A 502 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 669 ASP cc_start: 0.7689 (m-30) cc_final: 0.7483 (m-30) REVERT: A 712 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7835 (ttm110) REVERT: B 244 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: G 1 MET cc_start: 0.8352 (ptp) cc_final: 0.8088 (ptm) REVERT: G 59 LYS cc_start: 0.7903 (tptp) cc_final: 0.7309 (tptt) REVERT: G 151 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8121 (t0) REVERT: J 196 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6031 (mp0) REVERT: J 206 GLU cc_start: 0.1713 (OUTLIER) cc_final: 0.1285 (tm-30) REVERT: J 270 ILE cc_start: 0.5703 (OUTLIER) cc_final: 0.4981 (tt) outliers start: 68 outliers final: 33 residues processed: 209 average time/residue: 0.4664 time to fit residues: 113.7467 Evaluate side-chains 190 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 203 PHE Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN A 734 ASN B 152 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107786 restraints weight = 45158.393| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.93 r_work: 0.3284 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17756 Z= 0.139 Angle : 0.683 11.603 24046 Z= 0.333 Chirality : 0.056 0.736 2708 Planarity : 0.003 0.040 2983 Dihedral : 11.223 140.140 2645 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.43 % Allowed : 18.42 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.08 (0.18), residues: 2065 helix: 0.56 (0.19), residues: 758 sheet: -0.80 (0.26), residues: 370 loop : -1.75 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 125 TYR 0.021 0.001 TYR H 55 PHE 0.027 0.001 PHE J 296 TRP 0.003 0.001 TRP A 334 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (17753) covalent geometry : angle 0.67306 / 0.33 (24040) SS BOND : bond 0.01320 / 0.65 ( 3) SS BOND : angle 7.31242 / 3.06 ( 6) hydrogen bonds : bond 0.03563 / 2.39 ( 679) hydrogen bonds : angle 5.13263 / 3.54 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: F 101 LEU cc_start: 0.9302 (tp) cc_final: 0.9096 (tp) REVERT: F 116 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: F 136 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: H 147 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: H 151 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8057 (p0) REVERT: H 153 ASP cc_start: 0.6850 (t0) cc_final: 0.6495 (t0) REVERT: A 356 ASP cc_start: 0.7857 (t0) cc_final: 0.7469 (t0) REVERT: A 447 MET cc_start: 0.8250 (ttm) cc_final: 0.7839 (mtp) REVERT: A 486 MET cc_start: 0.8565 (ptp) cc_final: 0.8308 (ptp) REVERT: A 502 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 503 MET cc_start: 0.8471 (ttp) cc_final: 0.8162 (ttm) REVERT: A 612 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 669 ASP cc_start: 0.7728 (m-30) cc_final: 0.7508 (m-30) REVERT: A 712 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7818 (ttm110) REVERT: B 244 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: J 157 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6368 (mt0) REVERT: J 196 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6076 (mp0) REVERT: J 206 GLU cc_start: 0.1687 (OUTLIER) cc_final: 0.1262 (tm-30) REVERT: J 270 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.4968 (tt) outliers start: 62 outliers final: 32 residues processed: 213 average time/residue: 0.4568 time to fit residues: 113.6648 Evaluate side-chains 189 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 80 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 44 optimal weight: 0.0050 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.142806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109445 restraints weight = 36757.333| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.64 r_work: 0.3324 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17756 Z= 0.129 Angle : 0.674 10.983 24046 Z= 0.328 Chirality : 0.055 0.704 2708 Planarity : 0.003 0.037 2983 Dihedral : 11.124 139.291 2645 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.04 % Allowed : 19.41 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.98 (0.18), residues: 2065 helix: 0.66 (0.19), residues: 758 sheet: -0.73 (0.26), residues: 362 loop : -1.71 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 125 TYR 0.022 0.001 TYR H 55 PHE 0.031 0.001 PHE A 728 TRP 0.004 0.001 TRP J 228 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (17753) covalent geometry : angle 0.66434 / 0.32 (24040) SS BOND : bond 0.01175 / 0.58 ( 3) SS BOND : angle 7.05270 / 2.98 ( 6) hydrogen bonds : bond 0.03460 / 2.33 ( 679) hydrogen bonds : angle 5.03522 / 3.49 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 116 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6913 (pm20) REVERT: F 136 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: H 147 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: H 151 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8012 (p0) REVERT: H 153 ASP cc_start: 0.6863 (t0) cc_final: 0.6557 (t0) REVERT: A 181 MET cc_start: 0.8867 (tmm) cc_final: 0.8584 (ttt) REVERT: A 356 ASP cc_start: 0.7813 (t0) cc_final: 0.7415 (t0) REVERT: A 447 MET cc_start: 0.8221 (ttm) cc_final: 0.7961 (mtp) REVERT: A 502 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 503 MET cc_start: 0.8500 (ttp) cc_final: 0.8160 (ttm) REVERT: A 712 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7838 (ttm110) REVERT: B 244 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: G 151 ASN cc_start: 0.8592 (p0) cc_final: 0.8195 (t0) REVERT: J 196 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6535 (mp0) REVERT: J 206 GLU cc_start: 0.1718 (OUTLIER) cc_final: 0.1332 (tm-30) REVERT: J 270 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5054 (tt) outliers start: 55 outliers final: 32 residues processed: 193 average time/residue: 0.4432 time to fit residues: 100.5857 Evaluate side-chains 181 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 135 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN H 180 HIS A 45 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105110 restraints weight = 34800.449| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.58 r_work: 0.3255 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17756 Z= 0.215 Angle : 0.757 12.106 24046 Z= 0.368 Chirality : 0.060 0.876 2708 Planarity : 0.004 0.044 2983 Dihedral : 11.457 143.786 2645 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.37 % Allowed : 19.58 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.18), residues: 2065 helix: 0.54 (0.19), residues: 753 sheet: -0.83 (0.26), residues: 368 loop : -1.78 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 125 TYR 0.023 0.002 TYR H 55 PHE 0.028 0.002 PHE J 296 TRP 0.008 0.001 TRP A 186 HIS 0.005 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (17753) covalent geometry : angle 0.74802 / 0.36 (24040) SS BOND : bond 0.01728 / 0.85 ( 3) SS BOND : angle 7.54628 / 3.18 ( 6) hydrogen bonds : bond 0.04026 / 2.71 ( 679) hydrogen bonds : angle 5.27862 / 3.66 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: I 174 PHE cc_start: 0.8194 (m-80) cc_final: 0.7978 (m-80) REVERT: I 177 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7178 (tp) REVERT: F 116 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: F 136 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: H 147 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: H 151 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8160 (p0) REVERT: H 153 ASP cc_start: 0.6906 (t0) cc_final: 0.6667 (t0) REVERT: A 181 MET cc_start: 0.8897 (tmm) cc_final: 0.8624 (ttt) REVERT: A 356 ASP cc_start: 0.7957 (t0) cc_final: 0.7588 (t0) REVERT: A 447 MET cc_start: 0.8354 (ttm) cc_final: 0.8132 (ttm) REVERT: A 502 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 503 MET cc_start: 0.8557 (ttp) cc_final: 0.8229 (ttm) REVERT: A 712 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7814 (ttm110) REVERT: B 244 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: J 157 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6446 (mt0) REVERT: J 196 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6368 (mp0) REVERT: J 206 GLU cc_start: 0.1498 (OUTLIER) cc_final: 0.1126 (tm-30) REVERT: J 270 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.4952 (tt) outliers start: 61 outliers final: 34 residues processed: 195 average time/residue: 0.4592 time to fit residues: 104.2473 Evaluate side-chains 182 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 61 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 3 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 180 HIS A 45 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107133 restraints weight = 34515.883| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.53 r_work: 0.3284 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17756 Z= 0.162 Angle : 0.717 11.583 24046 Z= 0.349 Chirality : 0.057 0.780 2708 Planarity : 0.003 0.040 2983 Dihedral : 11.358 141.646 2645 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.88 % Allowed : 20.58 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.05 (0.18), residues: 2065 helix: 0.59 (0.19), residues: 756 sheet: -0.79 (0.26), residues: 368 loop : -1.74 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 125 TYR 0.022 0.001 TYR H 55 PHE 0.030 0.001 PHE A 728 TRP 0.004 0.001 TRP A 186 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (17753) covalent geometry : angle 0.70778 / 0.34 (24040) SS BOND : bond 0.01455 / 0.72 ( 3) SS BOND : angle 7.32587 / 3.08 ( 6) hydrogen bonds : bond 0.03708 / 2.49 ( 679) hydrogen bonds : angle 5.16833 / 3.58 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: F 116 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: F 136 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: H 147 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: H 151 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8170 (p0) REVERT: H 153 ASP cc_start: 0.6894 (t0) cc_final: 0.6591 (t0) REVERT: A 181 MET cc_start: 0.8874 (tmm) cc_final: 0.8597 (ttt) REVERT: A 356 ASP cc_start: 0.7890 (t0) cc_final: 0.7502 (t0) REVERT: A 447 MET cc_start: 0.8313 (ttm) cc_final: 0.8050 (mtp) REVERT: A 503 MET cc_start: 0.8559 (ttp) cc_final: 0.8230 (ttm) REVERT: A 712 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7797 (ttm110) REVERT: B 244 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: J 196 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6420 (mp0) REVERT: J 206 GLU cc_start: 0.1414 (OUTLIER) cc_final: 0.1024 (tm-30) REVERT: J 270 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5110 (tt) outliers start: 52 outliers final: 30 residues processed: 189 average time/residue: 0.4334 time to fit residues: 95.9077 Evaluate side-chains 178 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 chunk 173 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 180 HIS A 45 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.139772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106145 restraints weight = 44585.524| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.10 r_work: 0.3242 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17756 Z= 0.181 Angle : 0.734 11.653 24046 Z= 0.356 Chirality : 0.058 0.806 2708 Planarity : 0.004 0.037 2983 Dihedral : 11.376 141.773 2645 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.60 % Allowed : 21.07 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 2065 helix: 0.58 (0.19), residues: 756 sheet: -0.80 (0.26), residues: 367 loop : -1.71 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 125 TYR 0.023 0.001 TYR H 55 PHE 0.028 0.001 PHE J 296 TRP 0.005 0.001 TRP A 186 HIS 0.005 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (17753) covalent geometry : angle 0.72426 / 0.35 (24040) SS BOND : bond 0.01553 / 0.77 ( 3) SS BOND : angle 7.39866 / 3.12 ( 6) hydrogen bonds : bond 0.03800 / 2.55 ( 679) hydrogen bonds : angle 5.19978 / 3.60 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6478.98 seconds wall clock time: 111 minutes 23.45 seconds (6683.45 seconds total)