Starting phenix.real_space_refine on Sun Sep 13 08:30:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.map" model { file = "/net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xn7_22269/09_2026/6xn7_22269.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 73 5.49 5 S 52 5.16 5 C 13874 2.51 5 N 3771 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s 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: 22212 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6033 Classifications: {'peptide': 746} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 733} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2239 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 277, 2237 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 265} 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: 277, 2237 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 265} 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: 2284 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "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: "J" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Chain: "R" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 6, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 18, 'rna3p': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "T" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 793 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 17, 'rna3p_pyr': 12} Link IDs: {'rna2p': 8, 'rna3p': 28} Time building chain proxies: 5.52, per 1000 atoms: 0.25 Number of scatterers: 22212 At special positions: 0 Unit cell: (118.14, 140.694, 206.208, 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 52 16.00 P 73 15.00 O 4442 8.00 N 3771 7.00 C 13874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 405 " distance=2.06 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 418 " distance=1.97 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 421 " distance=2.15 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.08 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=1.95 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=1.97 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 31 sheets defined 43.9% alpha, 13.5% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.576A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.825A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.795A pdb=" N CYS A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.900A pdb=" N SER A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.793A pdb=" N SER A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.362A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.732A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.733A pdb=" N VAL A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 200 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 201 " --> pdb=" O LEU A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 202 through 225 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.739A pdb=" N GLU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.770A pdb=" N ASP A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 269 through 295 removed outlier: 3.764A pdb=" N LEU A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 339 removed outlier: 3.879A pdb=" N ASP A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 4.140A 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 431 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.772A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.712A pdb=" N ASN A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 485' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.923A pdb=" N SER A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.243A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 637 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 668 through 681 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.781A pdb=" N LEU A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 3.842A pdb=" N ASN A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 removed outlier: 3.869A pdb=" N ILE A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 739 through 754 removed outlier: 3.554A pdb=" N LEU A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.683A pdb=" N GLY B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.544A pdb=" N PHE B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.812A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'F' and resid 45 through 62 removed outlier: 3.649A pdb=" N ASN F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 82 removed outlier: 3.869A pdb=" N LEU F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 157 through 173 Processing helix chain 'F' and resid 204 through 213 removed outlier: 4.017A pdb=" N LEU F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 63 removed outlier: 3.514A pdb=" N LEU H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.930A pdb=" N ASP H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.604A 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 180 through 184 Processing helix chain 'H' and resid 205 through 213 removed outlier: 3.682A pdb=" N ILE H 211 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.878A pdb=" N ASP G 73 " --> pdb=" O PRO G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 removed outlier: 3.529A pdb=" N PHE G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 205 through 212 Processing helix chain 'I' and resid 45 through 62 Processing helix chain 'I' and resid 69 through 73 removed outlier: 4.035A pdb=" N ASP I 73 " --> pdb=" O PRO I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 4.789A pdb=" N LEU I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 157 through 174 removed outlier: 3.584A pdb=" N PHE I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.509A pdb=" N ARG I 183 " --> pdb=" O HIS I 180 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY I 184 " --> pdb=" O GLY I 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 180 through 184' Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.541A pdb=" N ASN I 209 " --> pdb=" O ILE I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 50 removed outlier: 3.911A pdb=" N PHE J 45 " --> pdb=" O ASP J 41 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 64 Processing helix chain 'J' and resid 70 through 74 removed outlier: 3.676A pdb=" N ASN J 74 " --> pdb=" O TYR J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 140 removed outlier: 3.711A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 226 Processing helix chain 'J' and resid 275 through 280 removed outlier: 3.612A pdb=" N LYS J 279 " --> pdb=" O GLY J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 303 removed outlier: 4.000A pdb=" N GLN J 301 " --> pdb=" O ASP J 297 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 4.276A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.595A pdb=" N GLU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.592A pdb=" N ILE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 72 removed outlier: 3.727A pdb=" N LYS D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.550A pdb=" N GLU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 55 through 73 removed outlier: 4.572A pdb=" N LYS E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.519A pdb=" N LEU E 84 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.543A pdb=" N LYS E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 125 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA2, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.594A pdb=" N THR A 350 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 348 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.302A pdb=" N ILE A 473 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.678A pdb=" N SER A 607 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.678A pdb=" N SER A 607 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 65 removed outlier: 6.213A pdb=" N PHE B 59 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU B 160 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP B 61 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU B 158 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 7 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 132 Processing sheet with id=AA9, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 275 Processing sheet with id=AB3, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.821A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 120 Processing sheet with id=AB7, first strand: chain 'H' and resid 188 through 197 removed outlier: 5.500A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE H 146 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU H 147 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN H 97 " --> pdb=" O GLU H 147 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY G 184 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AC1, first strand: chain 'G' and resid 94 through 95 removed outlier: 3.557A pdb=" N GLY G 7 " --> pdb=" O PHE G 146 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS G 2 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR G 197 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 4 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL G 195 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU G 6 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU G 193 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC3, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC4, first strand: chain 'I' and resid 94 through 95 removed outlier: 3.726A pdb=" N PHE I 146 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR I 8 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN I 192 " --> pdb=" O THR I 8 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 10 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE I 190 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'I' and resid 115 through 120 Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.529A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC9, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.862A pdb=" N GLU J 189 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 174 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN J 173 " --> pdb=" O ASN J 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 29 through 31 removed outlier: 3.809A pdb=" N PHE J 30 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS J 38 " --> pdb=" O PHE J 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'D' and resid 13 through 15 902 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 6817 1.34 - 1.47: 6051 1.47 - 1.61: 9770 1.61 - 1.75: 5 1.75 - 1.88: 97 Bond restraints: 22740 Sorted by residual: bond pdb=" C ASN H 68 " pdb=" N GLU H 69 " ideal model delta sigma weight residual 1.331 1.234 0.096 1.48e-02 4.57e+03 4.23e+01 bond pdb=" CG1 ILE G 77 " pdb=" CD1 ILE G 77 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.60e+00 bond pdb=" CA GLU C 19 " pdb=" CB GLU C 19 " ideal model delta sigma weight residual 1.527 1.562 -0.035 1.30e-02 5.92e+03 7.23e+00 bond pdb=" CG1 ILE C 37 " pdb=" CD1 ILE C 37 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.36e+00 bond pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 5.02e+00 ... (remaining 22735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 30120 3.11 - 6.21: 735 6.21 - 9.32: 94 9.32 - 12.42: 13 12.42 - 15.53: 3 Bond angle restraints: 30965 Sorted by residual: angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 121.70 137.23 -15.53 1.80e+00 3.09e-01 7.44e+01 angle pdb=" N GLY G 14 " pdb=" CA GLY G 14 " pdb=" C GLY G 14 " ideal model delta sigma weight residual 112.50 120.04 -7.54 1.16e+00 7.43e-01 4.23e+01 angle pdb=" C ASN G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta sigma weight residual 121.70 133.27 -11.57 1.80e+00 3.09e-01 4.13e+01 angle pdb=" C ASN H 68 " pdb=" N GLU H 69 " pdb=" CA GLU H 69 " ideal model delta sigma weight residual 121.03 130.39 -9.36 1.60e+00 3.91e-01 3.42e+01 angle pdb=" C3' A R 32 " pdb=" O3' A R 32 " pdb=" P A R 33 " ideal model delta sigma weight residual 119.70 126.53 -6.83 1.20e+00 6.94e-01 3.24e+01 ... (remaining 30960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 13066 33.69 - 67.39: 494 67.39 - 101.08: 42 101.08 - 134.78: 0 134.78 - 168.47: 1 Dihedral angle restraints: 13603 sinusoidal: 6106 harmonic: 7497 Sorted by residual: dihedral pdb=" C4' A T 8 " pdb=" C3' A T 8 " pdb=" C2' A T 8 " pdb=" C1' A T 8 " ideal model delta sinusoidal sigma weight residual 36.34 -39.67 76.01 1 3.10e+00 1.04e-01 7.58e+02 dihedral pdb=" C4' A R 21 " pdb=" C3' A R 21 " pdb=" C2' A R 21 " pdb=" C1' A R 21 " ideal model delta sinusoidal sigma weight residual 36.35 -39.57 75.91 1 3.10e+00 1.04e-01 7.56e+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 -38.88 75.22 1 3.10e+00 1.04e-01 7.44e+02 ... (remaining 13600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2996 0.092 - 0.184: 395 0.184 - 0.276: 96 0.276 - 0.368: 33 0.368 - 0.460: 5 Chirality restraints: 3525 Sorted by residual: chirality pdb=" P A R 33 " pdb=" OP1 A R 33 " pdb=" OP2 A R 33 " pdb=" O5' A R 33 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB ILE A 532 " pdb=" CA ILE A 532 " pdb=" CG1 ILE A 532 " pdb=" CG2 ILE A 532 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C1' A R 25 " pdb=" O4' A R 25 " pdb=" C2' A R 25 " pdb=" N9 A R 25 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.41 2.00e-01 2.50e+01 4.17e+00 ... (remaining 3522 not shown) Planarity restraints: 3706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 111 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ASN G 111 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN G 111 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL G 112 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 97 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" CD GLU E 97 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU E 97 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU E 97 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 69 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO H 70 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 70 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 70 " -0.043 5.00e-02 4.00e+02 ... (remaining 3703 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4350 2.77 - 3.30: 20424 3.30 - 3.83: 38078 3.83 - 4.37: 45383 4.37 - 4.90: 77808 Nonbonded interactions: 186043 Sorted by model distance: nonbonded pdb=" O SER I 24 " pdb=" OH TYR D 89 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B 246 " pdb=" O LYS B 278 " model vdw 2.244 3.040 nonbonded pdb=" O TYR A 383 " pdb=" OH TYR B 232 " model vdw 2.258 3.040 nonbonded pdb=" OG SER I 47 " pdb=" OP1 G R 27 " model vdw 2.262 3.040 nonbonded pdb=" OG SER H 47 " pdb=" OP1 A R 21 " model vdw 2.267 3.040 ... (remaining 186038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 16 through 43 or resid 50 through 146)) selection = (chain 'D' and (resid 16 through 43 or resid 50 through 146)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 65 or resid 73 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.090 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.008 0.122 22746 Z= 0.336 Angle : 1.240 32.472 30977 Z= 0.649 Chirality : 0.076 0.460 3525 Planarity : 0.006 0.078 3706 Dihedral : 16.814 168.471 8755 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.09 % Favored : 92.87 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.47 (0.14), residues: 2540 helix: -1.97 (0.13), residues: 1047 sheet: -2.45 (0.23), residues: 385 loop : -2.44 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG E 124 TYR 0.045 0.003 TYR J 69 PHE 0.033 0.003 PHE A 73 TRP 0.010 0.002 TRP J 228 HIS 0.007 0.002 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.33 (22740) covalent geometry : angle 1.15276 / 0.61 (30965) SS BOND : bond 0.07299 / 3.88 ( 6) SS BOND : angle 23.20397 / 12.80 ( 12) hydrogen bonds : bond 0.17365 / 11.45 ( 943) hydrogen bonds : angle 8.09497 / 5.67 ( 2685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.882 Fit side-chains REVERT: J 48 TYR cc_start: 0.4106 (t80) cc_final: 0.3887 (t80) REVERT: C 49 GLU cc_start: 0.7685 (pm20) cc_final: 0.6984 (pp20) REVERT: D 51 LYS cc_start: 0.7707 (pttt) cc_final: 0.7387 (mtmt) REVERT: E 91 LYS cc_start: 0.6947 (mtmm) cc_final: 0.6556 (mtmm) REVERT: E 93 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6952 (mtmt) outliers start: 2 outliers final: 2 residues processed: 234 average time/residue: 0.1803 time to fit residues: 65.1454 Evaluate side-chains 173 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain E residue 109 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN A 555 ASN A 707 GLN B 242 GLN H 16 HIS C 65 ASN C 122 ASN E 22 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088631 restraints weight = 63437.133| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.94 r_work: 0.3152 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 22746 Z= 0.213 Angle : 1.033 31.682 30977 Z= 0.479 Chirality : 0.087 1.772 3525 Planarity : 0.004 0.053 3706 Dihedral : 12.908 163.408 3679 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.85 % Allowed : 6.76 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.15), residues: 2540 helix: -0.59 (0.15), residues: 1064 sheet: -2.26 (0.23), residues: 416 loop : -2.28 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 35 TYR 0.016 0.001 TYR E 96 PHE 0.020 0.002 PHE C 129 TRP 0.012 0.001 TRP J 228 HIS 0.003 0.001 HIS F 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (22740) covalent geometry : angle 0.93254 / 0.43 (30965) SS BOND : bond 0.09193 / 4.69 ( 6) SS BOND : angle 22.54529 / 12.27 ( 12) hydrogen bonds : bond 0.04461 / 2.99 ( 943) hydrogen bonds : angle 5.55858 / 3.97 ( 2685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 707 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7684 (mm110) REVERT: A 709 ASN cc_start: 0.7664 (m-40) cc_final: 0.7408 (m-40) REVERT: G 88 LYS cc_start: 0.8147 (mttp) cc_final: 0.7764 (tptm) REVERT: J 38 HIS cc_start: 0.7084 (m-70) cc_final: 0.6848 (m-70) REVERT: C 28 ASP cc_start: 0.7377 (m-30) cc_final: 0.7171 (t0) REVERT: D 51 LYS cc_start: 0.8194 (pttt) cc_final: 0.7847 (mtmt) REVERT: E 22 ASN cc_start: 0.7720 (t0) cc_final: 0.7503 (t0) REVERT: E 93 LYS cc_start: 0.7081 (mtpt) cc_final: 0.6597 (mtmt) outliers start: 19 outliers final: 10 residues processed: 202 average time/residue: 0.1640 time to fit residues: 53.0652 Evaluate side-chains 172 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 707 GLN Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 82 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN I 151 ASN D 73 ASN E 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086012 restraints weight = 66161.188| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.97 r_work: 0.3119 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 22746 Z= 0.224 Angle : 0.944 31.145 30977 Z= 0.448 Chirality : 0.076 1.462 3525 Planarity : 0.004 0.046 3706 Dihedral : 12.897 176.724 3675 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.92 % Allowed : 10.34 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.98 (0.16), residues: 2540 helix: -0.07 (0.16), residues: 1068 sheet: -2.11 (0.23), residues: 409 loop : -2.24 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 183 TYR 0.021 0.002 TYR A 229 PHE 0.021 0.002 PHE A 36 TRP 0.011 0.001 TRP J 228 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (22740) covalent geometry : angle 0.83457 / 0.40 (30965) SS BOND : bond 0.09663 / 4.87 ( 6) SS BOND : angle 22.37599 / 12.09 ( 12) hydrogen bonds : bond 0.04016 / 2.68 ( 943) hydrogen bonds : angle 5.18598 / 3.71 ( 2685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.831 Fit side-chains REVERT: J 69 TYR cc_start: 0.2874 (p90) cc_final: 0.0883 (p90) REVERT: C 28 ASP cc_start: 0.7392 (m-30) cc_final: 0.7156 (t0) REVERT: C 40 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7163 (pttt) REVERT: D 51 LYS cc_start: 0.7613 (pttt) cc_final: 0.7303 (mtmt) REVERT: E 22 ASN cc_start: 0.7703 (t0) cc_final: 0.7498 (t0) REVERT: E 89 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6460 (t80) REVERT: E 93 LYS cc_start: 0.7141 (mtpt) cc_final: 0.6424 (mtmt) REVERT: E 135 TYR cc_start: 0.7829 (t80) cc_final: 0.7486 (t80) outliers start: 43 outliers final: 26 residues processed: 197 average time/residue: 0.1569 time to fit residues: 49.5890 Evaluate side-chains 182 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 89 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 181 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 706 GLN I 151 ASN J 282 HIS D 65 ASN E 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085201 restraints weight = 63359.020| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.01 r_work: 0.3106 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 22746 Z= 0.235 Angle : 0.935 30.984 30977 Z= 0.444 Chirality : 0.075 1.442 3525 Planarity : 0.004 0.044 3706 Dihedral : 12.994 178.656 3675 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.15 % Allowed : 12.66 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.81 (0.16), residues: 2540 helix: 0.13 (0.16), residues: 1073 sheet: -2.06 (0.23), residues: 403 loop : -2.22 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 79 TYR 0.016 0.002 TYR A 229 PHE 0.021 0.002 PHE C 129 TRP 0.010 0.001 TRP J 228 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (22740) covalent geometry : angle 0.82441 / 0.39 (30965) SS BOND : bond 0.09679 / 4.85 ( 6) SS BOND : angle 22.37747 / 12.09 ( 12) hydrogen bonds : bond 0.03929 / 2.62 ( 943) hydrogen bonds : angle 5.09070 / 3.64 ( 2685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.835 Fit side-chains REVERT: A 473 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7687 (mp) REVERT: H 89 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7598 (tt) REVERT: C 28 ASP cc_start: 0.7462 (m-30) cc_final: 0.7153 (t0) REVERT: D 51 LYS cc_start: 0.7962 (pttt) cc_final: 0.7649 (mtmt) REVERT: E 89 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6442 (t80) REVERT: E 93 LYS cc_start: 0.7000 (mtpt) cc_final: 0.6321 (mtmt) REVERT: E 135 TYR cc_start: 0.7792 (t80) cc_final: 0.7462 (t80) outliers start: 48 outliers final: 28 residues processed: 193 average time/residue: 0.1619 time to fit residues: 49.6891 Evaluate side-chains 180 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 71 TYR Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 89 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 230 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086415 restraints weight = 48936.298| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.64 r_work: 0.3139 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 22746 Z= 0.213 Angle : 0.903 30.981 30977 Z= 0.430 Chirality : 0.072 1.366 3525 Planarity : 0.004 0.044 3706 Dihedral : 13.053 179.926 3675 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.46 % Allowed : 14.50 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.68 (0.16), residues: 2540 helix: 0.28 (0.16), residues: 1073 sheet: -2.00 (0.23), residues: 402 loop : -2.19 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 183 TYR 0.013 0.001 TYR A 229 PHE 0.021 0.002 PHE C 129 TRP 0.010 0.001 TRP J 228 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (22740) covalent geometry : angle 0.78944 / 0.38 (30965) SS BOND : bond 0.09797 / 4.90 ( 6) SS BOND : angle 22.32980 / 12.06 ( 12) hydrogen bonds : bond 0.03743 / 2.49 ( 943) hydrogen bonds : angle 4.96459 / 3.56 ( 2685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 1.073 Fit side-chains REVERT: A 473 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7578 (mp) REVERT: H 183 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.6947 (mpp80) REVERT: J 69 TYR cc_start: 0.2978 (p90) cc_final: 0.2218 (p90) REVERT: C 121 MET cc_start: 0.8222 (mmm) cc_final: 0.7792 (mmm) REVERT: D 42 PHE cc_start: 0.6301 (t80) cc_final: 0.5999 (t80) REVERT: D 51 LYS cc_start: 0.8013 (pttt) cc_final: 0.7745 (mtmt) REVERT: E 89 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6451 (t80) REVERT: E 93 LYS cc_start: 0.7086 (mtpt) cc_final: 0.6096 (mtmt) REVERT: E 97 GLU cc_start: 0.8176 (mp0) cc_final: 0.7609 (mp0) REVERT: E 135 TYR cc_start: 0.7793 (t80) cc_final: 0.7481 (t80) outliers start: 55 outliers final: 33 residues processed: 201 average time/residue: 0.1683 time to fit residues: 54.1382 Evaluate side-chains 191 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain E residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 ASN H 151 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087277 restraints weight = 56636.075| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.79 r_work: 0.3152 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 22746 Z= 0.187 Angle : 0.874 31.127 30977 Z= 0.416 Chirality : 0.068 1.314 3525 Planarity : 0.003 0.045 3706 Dihedral : 12.956 179.906 3675 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.73 % Allowed : 14.81 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.52 (0.16), residues: 2540 helix: 0.44 (0.16), residues: 1074 sheet: -1.92 (0.23), residues: 402 loop : -2.14 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 700 TYR 0.012 0.001 TYR A 364 PHE 0.021 0.001 PHE C 129 TRP 0.009 0.001 TRP J 228 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (22740) covalent geometry : angle 0.75554 / 0.36 (30965) SS BOND : bond 0.09810 / 4.90 ( 6) SS BOND : angle 22.32115 / 12.05 ( 12) hydrogen bonds : bond 0.03609 / 2.40 ( 943) hydrogen bonds : angle 4.83840 / 3.47 ( 2685) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 0.814 Fit side-chains REVERT: A 60 ILE cc_start: 0.8141 (mm) cc_final: 0.7827 (mt) REVERT: A 473 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7589 (mp) REVERT: H 89 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7581 (tt) REVERT: H 183 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.6865 (mpp80) REVERT: J 227 LYS cc_start: 0.0305 (OUTLIER) cc_final: -0.0022 (pttt) REVERT: C 121 MET cc_start: 0.8158 (mmm) cc_final: 0.7689 (mmm) REVERT: C 139 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8621 (tt) REVERT: D 42 PHE cc_start: 0.6202 (t80) cc_final: 0.5946 (t80) REVERT: D 51 LYS cc_start: 0.8129 (pttt) cc_final: 0.7859 (mtmt) REVERT: E 58 ARG cc_start: 0.6504 (tpt-90) cc_final: 0.6178 (tpt-90) REVERT: E 89 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6436 (t80) REVERT: E 93 LYS cc_start: 0.6976 (mtpt) cc_final: 0.6038 (mtmt) REVERT: E 97 GLU cc_start: 0.8226 (mp0) cc_final: 0.7632 (mp0) outliers start: 61 outliers final: 38 residues processed: 220 average time/residue: 0.1719 time to fit residues: 59.5859 Evaluate side-chains 205 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain E residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 23 optimal weight: 0.0070 chunk 92 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 151 ASN E 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085808 restraints weight = 52784.795| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.74 r_work: 0.3125 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 22746 Z= 0.244 Angle : 0.921 31.003 30977 Z= 0.439 Chirality : 0.072 1.396 3525 Planarity : 0.004 0.051 3706 Dihedral : 13.080 179.298 3675 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.18 % Allowed : 15.12 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.58 (0.16), residues: 2540 helix: 0.41 (0.16), residues: 1073 sheet: -2.09 (0.24), residues: 377 loop : -2.14 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 100 TYR 0.023 0.002 TYR E 135 PHE 0.021 0.002 PHE C 129 TRP 0.009 0.001 TRP J 228 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (22740) covalent geometry : angle 0.80975 / 0.39 (30965) SS BOND : bond 0.09729 / 4.85 ( 6) SS BOND : angle 22.35504 / 12.06 ( 12) hydrogen bonds : bond 0.03806 / 2.55 ( 943) hydrogen bonds : angle 4.93196 / 3.53 ( 2685) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 0.903 Fit side-chains REVERT: A 60 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7870 (mt) REVERT: A 473 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7656 (mp) REVERT: B 234 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8595 (mp) REVERT: H 183 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.6902 (mpp80) REVERT: G 55 TYR cc_start: 0.8891 (t80) cc_final: 0.8580 (t80) REVERT: I 74 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: J 227 LYS cc_start: 0.0421 (OUTLIER) cc_final: 0.0116 (pttt) REVERT: C 121 MET cc_start: 0.8183 (mmm) cc_final: 0.7755 (mmm) REVERT: C 139 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8665 (tt) REVERT: D 42 PHE cc_start: 0.6342 (t80) cc_final: 0.6102 (t80) REVERT: D 51 LYS cc_start: 0.8223 (pttt) cc_final: 0.7921 (mtmt) REVERT: E 89 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6427 (t80) REVERT: E 93 LYS cc_start: 0.7113 (mtpt) cc_final: 0.6066 (mtmt) REVERT: E 97 GLU cc_start: 0.8162 (mp0) cc_final: 0.7538 (mp0) outliers start: 71 outliers final: 47 residues processed: 218 average time/residue: 0.1672 time to fit residues: 58.3539 Evaluate side-chains 209 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain E residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 0.9980 chunk 228 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 112 optimal weight: 0.0060 chunk 142 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 194 optimal weight: 0.0770 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN H 151 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 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 = 0.3668 r_free = 0.3668 target = 0.110860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092331 restraints weight = 56311.644| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.88 r_work: 0.3258 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 22746 Z= 0.140 Angle : 0.830 31.341 30977 Z= 0.394 Chirality : 0.062 1.270 3525 Planarity : 0.003 0.045 3706 Dihedral : 12.570 177.194 3675 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.06 % Allowed : 16.20 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.25 (0.16), residues: 2540 helix: 0.69 (0.16), residues: 1075 sheet: -1.94 (0.24), residues: 391 loop : -1.96 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 700 TYR 0.018 0.001 TYR J 69 PHE 0.022 0.001 PHE A 327 TRP 0.010 0.001 TRP J 228 HIS 0.005 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22740) covalent geometry : angle 0.70585 / 0.33 (30965) SS BOND : bond 0.09986 / 5.01 ( 6) SS BOND : angle 22.23955 / 12.01 ( 12) hydrogen bonds : bond 0.03287 / 2.16 ( 943) hydrogen bonds : angle 4.63300 / 3.33 ( 2685) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.885 Fit side-chains REVERT: A 60 ILE cc_start: 0.7913 (mm) cc_final: 0.7610 (mt) REVERT: A 555 ASN cc_start: 0.7682 (m-40) cc_final: 0.7336 (t0) REVERT: A 557 LEU cc_start: 0.8457 (pp) cc_final: 0.8106 (mt) REVERT: H 15 MET cc_start: 0.9302 (tmm) cc_final: 0.9043 (tmm) REVERT: H 67 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7419 (mp) REVERT: H 89 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7294 (tt) REVERT: H 109 THR cc_start: 0.8930 (m) cc_final: 0.8675 (p) REVERT: H 183 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.6867 (mpp80) REVERT: G 55 TYR cc_start: 0.8754 (t80) cc_final: 0.8530 (t80) REVERT: G 88 LYS cc_start: 0.7954 (mttp) cc_final: 0.7601 (tptm) REVERT: I 74 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7308 (mm-40) REVERT: J 86 TYR cc_start: 0.5743 (p90) cc_final: 0.5373 (p90) REVERT: J 227 LYS cc_start: -0.0402 (OUTLIER) cc_final: -0.0695 (pttt) REVERT: C 121 MET cc_start: 0.8120 (mmm) cc_final: 0.7510 (mmm) REVERT: D 51 LYS cc_start: 0.8160 (pttt) cc_final: 0.7864 (mtmt) REVERT: E 51 LYS cc_start: 0.6476 (mmpt) cc_final: 0.5947 (ptmt) REVERT: E 89 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6334 (t80) REVERT: E 93 LYS cc_start: 0.7149 (mtpt) cc_final: 0.6174 (mtmt) REVERT: E 97 GLU cc_start: 0.8322 (mp0) cc_final: 0.7699 (mp0) outliers start: 46 outliers final: 28 residues processed: 241 average time/residue: 0.1686 time to fit residues: 64.2465 Evaluate side-chains 208 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain E residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 88 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 223 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 256 optimal weight: 8.9990 chunk 6 optimal weight: 0.0470 overall best weight: 2.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN H 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087715 restraints weight = 63259.678| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.02 r_work: 0.3159 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 22746 Z= 0.184 Angle : 0.861 31.194 30977 Z= 0.410 Chirality : 0.066 1.252 3525 Planarity : 0.003 0.050 3706 Dihedral : 12.696 178.750 3675 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.97 % Allowed : 16.73 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.21 (0.16), residues: 2540 helix: 0.69 (0.16), residues: 1075 sheet: -1.86 (0.24), residues: 384 loop : -1.93 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 58 TYR 0.024 0.001 TYR E 135 PHE 0.023 0.001 PHE A 327 TRP 0.009 0.001 TRP J 228 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (22740) covalent geometry : angle 0.74132 / 0.35 (30965) SS BOND : bond 0.09818 / 4.91 ( 6) SS BOND : angle 22.30320 / 12.04 ( 12) hydrogen bonds : bond 0.03426 / 2.28 ( 943) hydrogen bonds : angle 4.69098 / 3.36 ( 2685) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.911 Fit side-chains REVERT: A 60 ILE cc_start: 0.8023 (mm) cc_final: 0.7723 (mt) REVERT: B 234 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8540 (mp) REVERT: H 67 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7681 (mp) REVERT: H 89 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7577 (tt) REVERT: H 183 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.6816 (mpp80) REVERT: G 55 TYR cc_start: 0.8876 (t80) cc_final: 0.8633 (t80) REVERT: I 74 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: J 86 TYR cc_start: 0.5804 (p90) cc_final: 0.5425 (p90) REVERT: J 227 LYS cc_start: -0.0339 (OUTLIER) cc_final: -0.0622 (pttt) REVERT: C 110 ARG cc_start: 0.8873 (mtm-85) cc_final: 0.8586 (mtm-85) REVERT: C 121 MET cc_start: 0.8187 (mmm) cc_final: 0.7578 (mmm) REVERT: D 51 LYS cc_start: 0.8238 (pttt) cc_final: 0.7964 (mtmt) REVERT: E 51 LYS cc_start: 0.6484 (mmpt) cc_final: 0.5820 (mmpt) REVERT: E 89 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6268 (t80) REVERT: E 93 LYS cc_start: 0.6947 (mtpt) cc_final: 0.6039 (mtmt) REVERT: E 97 GLU cc_start: 0.8310 (mp0) cc_final: 0.7724 (mp0) outliers start: 44 outliers final: 30 residues processed: 203 average time/residue: 0.1650 time to fit residues: 53.3572 Evaluate side-chains 199 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain E residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 226 optimal weight: 0.8980 chunk 38 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.2451 > 50:) chunk 227 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 151 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088005 restraints weight = 62904.045| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.01 r_work: 0.3169 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 22746 Z= 0.172 Angle : 0.860 31.186 30977 Z= 0.408 Chirality : 0.065 1.237 3525 Planarity : 0.003 0.049 3706 Dihedral : 12.674 179.132 3675 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.92 % Allowed : 16.87 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.18 (0.16), residues: 2540 helix: 0.69 (0.16), residues: 1075 sheet: -1.86 (0.25), residues: 372 loop : -1.88 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 700 TYR 0.015 0.001 TYR J 69 PHE 0.022 0.001 PHE A 327 TRP 0.009 0.001 TRP J 228 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22740) covalent geometry : angle 0.73934 / 0.35 (30965) SS BOND : bond 0.09837 / 4.92 ( 6) SS BOND : angle 22.29462 / 12.03 ( 12) hydrogen bonds : bond 0.03388 / 2.24 ( 943) hydrogen bonds : angle 4.67796 / 3.35 ( 2685) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.902 Fit side-chains REVERT: A 60 ILE cc_start: 0.8002 (mm) cc_final: 0.7702 (mt) REVERT: A 555 ASN cc_start: 0.7867 (m-40) cc_final: 0.7411 (t0) REVERT: B 234 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8542 (mp) REVERT: H 67 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7688 (mp) REVERT: H 89 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7555 (tt) REVERT: H 109 THR cc_start: 0.8905 (m) cc_final: 0.8654 (p) REVERT: H 183 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.6766 (mpp80) REVERT: G 55 TYR cc_start: 0.8855 (t80) cc_final: 0.8622 (t80) REVERT: I 74 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: J 86 TYR cc_start: 0.5797 (p90) cc_final: 0.5457 (p90) REVERT: J 227 LYS cc_start: -0.0354 (OUTLIER) cc_final: -0.0655 (pttt) REVERT: C 110 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8598 (mtm-85) REVERT: C 121 MET cc_start: 0.8188 (mmm) cc_final: 0.7607 (mmm) REVERT: D 51 LYS cc_start: 0.8276 (pttt) cc_final: 0.7989 (mtmt) REVERT: E 51 LYS cc_start: 0.6465 (mmpt) cc_final: 0.5898 (ptmt) REVERT: E 89 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6287 (t80) REVERT: E 93 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6120 (mtmt) REVERT: E 97 GLU cc_start: 0.8293 (mp0) cc_final: 0.7761 (mp0) outliers start: 43 outliers final: 32 residues processed: 205 average time/residue: 0.1678 time to fit residues: 54.7303 Evaluate side-chains 204 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 183 ARG Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain E residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 157 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 123 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 80 optimal weight: 0.0670 chunk 214 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 151 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091025 restraints weight = 53146.975| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.83 r_work: 0.3236 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 22746 Z= 0.150 Angle : 0.834 31.272 30977 Z= 0.395 Chirality : 0.063 1.226 3525 Planarity : 0.003 0.047 3706 Dihedral : 12.489 179.628 3675 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.83 % Allowed : 17.14 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.08 (0.16), residues: 2540 helix: 0.76 (0.16), residues: 1078 sheet: -1.77 (0.25), residues: 372 loop : -1.85 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 700 TYR 0.016 0.001 TYR J 69 PHE 0.021 0.001 PHE A 327 TRP 0.010 0.001 TRP J 228 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22740) covalent geometry : angle 0.70912 / 0.34 (30965) SS BOND : bond 0.09886 / 4.96 ( 6) SS BOND : angle 22.26778 / 12.02 ( 12) hydrogen bonds : bond 0.03250 / 2.15 ( 943) hydrogen bonds : angle 4.58749 / 3.29 ( 2685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5954.29 seconds wall clock time: 103 minutes 5.31 seconds (6185.31 seconds total)