Starting phenix.real_space_refine on Sat Jul 4 13:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.map" model { file = "/net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zkp_14764/07_2026/7zkp_14764.cif" } resolution = 3.2 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= 0.010 sd= 0.099 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 8 5.49 5 S 80 5.16 5 C 13161 2.51 5 N 3145 2.21 5 O 3535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19929 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "L" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "X" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1274 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "1" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2426 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 290} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3776 Classifications: {'peptide': 469} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 461} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 909 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "6" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2763 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1749 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "b" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 3.80, per 1000 atoms: 0.19 Number of scatterers: 19929 At special positions: 0 Unit cell: (129.171, 118.307, 150.901, 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 80 16.00 P 8 15.00 O 3535 8.00 N 3145 7.00 C 13161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.03 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.04 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.04 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 5 sheets defined 69.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'D' and resid 4 through 34 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 43 through 58 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'L' and resid 2 through 19 Processing helix chain 'L' and resid 21 through 48 Processing helix chain 'L' and resid 49 through 79 removed outlier: 4.447A pdb=" N SER L 53 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 61 removed outlier: 5.235A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE U 41 " --> pdb=" O SER U 37 " (cutoff:3.500A) Proline residue: U 48 - end of helix removed outlier: 3.682A pdb=" N GLN U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 68 Processing helix chain 'U' and resid 68 through 90 removed outlier: 3.558A pdb=" N GLY U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 104 Processing helix chain 'U' and resid 107 through 110 removed outlier: 3.515A pdb=" N GLY U 110 " --> pdb=" O GLN U 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 107 through 110' Processing helix chain 'U' and resid 111 through 126 Processing helix chain 'U' and resid 141 through 145 Processing helix chain 'U' and resid 156 through 170 Processing helix chain 'W' and resid 32 through 96 removed outlier: 3.527A pdb=" N LEU W 69 " --> pdb=" O ALA W 65 " (cutoff:3.500A) Proline residue: W 71 - end of helix Processing helix chain 'X' and resid 27 through 34 Processing helix chain 'X' and resid 36 through 61 Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 71 through 99 Processing helix chain 'X' and resid 104 through 122 Processing helix chain 'X' and resid 132 through 144 Processing helix chain 'X' and resid 145 through 150 Processing helix chain '1' and resid 2 through 34 removed outlier: 3.766A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 58 removed outlier: 4.217A pdb=" N GLN 1 49 " --> pdb=" O TYR 1 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA 1 52 " --> pdb=" O LEU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 87 Proline residue: 1 77 - end of helix Processing helix chain '1' and resid 104 through 116 Processing helix chain '1' and resid 117 through 127 removed outlier: 3.802A pdb=" N LEU 1 121 " --> pdb=" O VAL 1 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER 1 127 " --> pdb=" O SER 1 123 " (cutoff:3.500A) Processing helix chain '1' and resid 129 through 159 removed outlier: 3.706A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 173 Processing helix chain '1' and resid 182 through 197 removed outlier: 3.692A pdb=" N THR 1 197 " --> pdb=" O SER 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 223 through 246 Processing helix chain '1' and resid 255 through 263 Processing helix chain '1' and resid 267 through 298 Processing helix chain '1' and resid 304 through 315 removed outlier: 3.645A pdb=" N CYS 1 312 " --> pdb=" O LEU 1 308 " (cutoff:3.500A) Processing helix chain '1' and resid 315 through 334 removed outlier: 3.714A pdb=" N LEU 1 319 " --> pdb=" O ILE 1 315 " (cutoff:3.500A) Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 2 through 15 removed outlier: 3.589A pdb=" N MET 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 19 No H-bonds generated for 'chain '2' and resid 17 through 19' Processing helix chain '2' and resid 20 through 39 Processing helix chain '2' and resid 40 through 50 removed outlier: 3.957A pdb=" N LEU 2 47 " --> pdb=" O LEU 2 44 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN 2 48 " --> pdb=" O LEU 2 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN 2 49 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 85 Processing helix chain '2' and resid 90 through 97 Processing helix chain '2' and resid 102 through 119 Processing helix chain '2' and resid 122 through 143 Processing helix chain '2' and resid 147 through 180 removed outlier: 3.565A pdb=" N ALA 2 153 " --> pdb=" O LYS 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 183 through 187 removed outlier: 3.947A pdb=" N SER 2 186 " --> pdb=" O THR 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 195 Processing helix chain '2' and resid 197 through 213 removed outlier: 3.793A pdb=" N ILE 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 228 Processing helix chain '2' and resid 229 through 237 removed outlier: 4.356A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 238 through 252 Processing helix chain '2' and resid 257 through 277 removed outlier: 3.729A pdb=" N LEU 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 2 277 " --> pdb=" O VAL 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 280 through 298 Processing helix chain '2' and resid 299 through 302 removed outlier: 3.812A pdb=" N LEU 2 302 " --> pdb=" O LEU 2 299 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 299 through 302' Processing helix chain '2' and resid 305 through 330 Processing helix chain '2' and resid 331 through 334 removed outlier: 3.535A pdb=" N ILE 2 334 " --> pdb=" O ILE 2 331 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 331 through 334' Processing helix chain '2' and resid 346 through 351 Processing helix chain '2' and resid 352 through 356 Processing helix chain '2' and resid 357 through 373 Processing helix chain '2' and resid 377 through 393 removed outlier: 3.559A pdb=" N PHE 2 381 " --> pdb=" O LEU 2 377 " (cutoff:3.500A) Processing helix chain '2' and resid 395 through 421 removed outlier: 3.786A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 436 through 453 Processing helix chain '2' and resid 456 through 468 Processing helix chain '3' and resid 3 through 25 Proline residue: 3 12 - end of helix removed outlier: 4.233A pdb=" N LEU 3 25 " --> pdb=" O VAL 3 21 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 72 removed outlier: 3.641A pdb=" N ILE 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix Processing helix chain '3' and resid 73 through 79 removed outlier: 3.538A pdb=" N SER 3 79 " --> pdb=" O PRO 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 108 removed outlier: 3.514A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 7 removed outlier: 3.688A pdb=" N TYR 6 7 " --> pdb=" O TYR 6 3 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 25 Processing helix chain '6' and resid 28 through 51 removed outlier: 3.512A pdb=" N SER 6 32 " --> pdb=" O ASN 6 28 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 66 removed outlier: 3.724A pdb=" N ILE 6 64 " --> pdb=" O ILE 6 60 " (cutoff:3.500A) Processing helix chain '6' and resid 66 through 81 removed outlier: 4.661A pdb=" N ASN 6 81 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 92 removed outlier: 3.994A pdb=" N ARG 6 92 " --> pdb=" O SER 6 89 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 89 through 92' Processing helix chain '6' and resid 93 through 110 Processing helix chain '6' and resid 111 through 117 Processing helix chain '6' and resid 118 through 128 removed outlier: 3.824A pdb=" N LEU 6 122 " --> pdb=" O LEU 6 118 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN 6 128 " --> pdb=" O GLU 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 156 Processing helix chain '6' and resid 158 through 181 Proline residue: 6 176 - end of helix Processing helix chain 'g' and resid 11 through 23 Processing helix chain 'g' and resid 23 through 51 removed outlier: 3.605A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Proline residue: g 45 - end of helix Processing helix chain 'b' and resid 3 through 25 Processing helix chain 'b' and resid 32 through 64 removed outlier: 3.790A pdb=" N LYS b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain '9' and resid 15 through 29 Processing helix chain '9' and resid 31 through 36 removed outlier: 4.345A pdb=" N ALA 9 35 " --> pdb=" O LYS 9 32 " (cutoff:3.500A) Processing helix chain '9' and resid 37 through 50 Processing helix chain '9' and resid 50 through 66 Processing helix chain '9' and resid 80 through 84 removed outlier: 3.615A pdb=" N ILE 9 84 " --> pdb=" O VAL 9 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.905A pdb=" N ALA C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 removed outlier: 3.600A pdb=" N THR C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET C 534 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 535 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 Processing helix chain 'C' and resid 555 through 565 removed outlier: 3.564A pdb=" N TYR C 565 " --> pdb=" O HIS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 3.873A pdb=" N GLU C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 600 removed outlier: 4.025A pdb=" N LYS C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 623 Processing helix chain 'C' and resid 630 through 642 removed outlier: 4.473A pdb=" N VAL C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 659 removed outlier: 3.566A pdb=" N ILE C 650 " --> pdb=" O TYR C 646 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 651 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 680 removed outlier: 3.595A pdb=" N VAL C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 695 removed outlier: 3.522A pdb=" N GLN C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 714 Processing helix chain 'C' and resid 717 through 732 Proline residue: C 729 - end of helix Processing helix chain 'C' and resid 736 through 750 removed outlier: 3.886A pdb=" N GLN C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 743 " --> pdb=" O ASN C 739 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 767 removed outlier: 3.578A pdb=" N LEU C 757 " --> pdb=" O TYR C 753 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 758 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 removed outlier: 3.797A pdb=" N ALA C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 800 removed outlier: 3.582A pdb=" N GLU C 793 " --> pdb=" O LYS C 789 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP C 795 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 809 removed outlier: 3.653A pdb=" N LEU C 805 " --> pdb=" O PRO C 801 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 807 " --> pdb=" O MET C 803 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 808 " --> pdb=" O TRP C 804 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 842 removed outlier: 3.540A pdb=" N GLU C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing sheet with id=AA1, first strand: chain '6' and resid 132 through 134 removed outlier: 3.639A pdb=" N TRP D 80 " --> pdb=" O PHE U 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.412A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 61 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 45 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.412A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 192 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG A 111 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 194 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 34 removed outlier: 5.426A pdb=" N VAL A 176 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A 123 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 130 " --> pdb=" O SER A 123 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3068 1.31 - 1.44: 5542 1.44 - 1.57: 11617 1.57 - 1.70: 20 1.70 - 1.84: 134 Bond restraints: 20381 Sorted by residual: bond pdb=" C LEU X 131 " pdb=" O LEU X 131 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.17e-02 7.31e+03 2.46e+01 bond pdb=" CB PLC 1 401 " pdb=" O3 PLC 1 401 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C11 CPL 2 501 " pdb=" O3 CPL 2 501 " ideal model delta sigma weight residual 1.327 1.417 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C' PLC 1 401 " pdb=" O2 PLC 1 401 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta sigma weight residual 1.532 1.455 0.078 1.79e-02 3.12e+03 1.89e+01 ... (remaining 20376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 27546 5.00 - 10.00: 64 10.00 - 15.00: 3 15.00 - 20.00: 3 20.00 - 25.00: 1 Bond angle restraints: 27617 Sorted by residual: angle pdb=" C39 CPL 2 501 " pdb=" C40 CPL 2 501 " pdb=" C41 CPL 2 501 " ideal model delta sigma weight residual 127.51 152.51 -25.00 3.00e+00 1.11e-01 6.94e+01 angle pdb=" C38 CPL 2 501 " pdb=" C39 CPL 2 501 " pdb=" C40 CPL 2 501 " ideal model delta sigma weight residual 127.82 111.74 16.08 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3P PLC 1 401 " pdb=" P PLC 1 401 " pdb=" O4P PLC 1 401 " ideal model delta sigma weight residual 93.62 109.53 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" N ILE 3 23 " pdb=" CA ILE 3 23 " pdb=" C ILE 3 23 " ideal model delta sigma weight residual 113.07 105.90 7.17 1.36e+00 5.41e-01 2.78e+01 angle pdb=" O3P CPL 2 501 " pdb=" P CPL 2 501 " pdb=" O4P CPL 2 501 " ideal model delta sigma weight residual 93.29 108.55 -15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 27612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 11811 35.63 - 71.26: 239 71.26 - 106.89: 13 106.89 - 142.52: 2 142.52 - 178.15: 1 Dihedral angle restraints: 12066 sinusoidal: 4868 harmonic: 7198 Sorted by residual: dihedral pdb=" N SER X 130 " pdb=" C SER X 130 " pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta harmonic sigma weight residual 122.80 109.23 13.57 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" N CPL 2 501 " pdb=" C4 CPL 2 501 " pdb=" C5 CPL 2 501 " pdb=" O4P CPL 2 501 " ideal model delta sinusoidal sigma weight residual 288.92 110.77 178.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C SER X 130 " pdb=" N SER X 130 " pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta harmonic sigma weight residual -122.60 -111.24 -11.36 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 12063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2602 0.054 - 0.107: 520 0.107 - 0.161: 43 0.161 - 0.214: 10 0.214 - 0.268: 3 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA THR X 128 " pdb=" N THR X 128 " pdb=" C THR X 128 " pdb=" CB THR X 128 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA SER X 130 " pdb=" N SER X 130 " pdb=" C SER X 130 " pdb=" CB SER X 130 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 PLC 1 401 " pdb=" C1 PLC 1 401 " pdb=" C3 PLC 1 401 " pdb=" O2 PLC 1 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.53 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 3175 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 23 " 0.077 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 24 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 804 " 0.021 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP C 804 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 804 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 804 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 804 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 804 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 804 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 804 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 804 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 804 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY X 127 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C GLY X 127 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY X 127 " -0.015 2.00e-02 2.50e+03 pdb=" N THR X 128 " -0.013 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 299 2.68 - 3.23: 19830 3.23 - 3.79: 32234 3.79 - 4.34: 43544 4.34 - 4.90: 70695 Nonbonded interactions: 166602 Sorted by model distance: nonbonded pdb=" O PHE X 151 " pdb=" OH TYR 2 73 " model vdw 2.119 3.040 nonbonded pdb=" OD1 ASP A 130 " pdb=" ND2 ASN A 158 " model vdw 2.137 3.120 nonbonded pdb=" NH2 ARG X 30 " pdb=" OD1 ASP X 111 " model vdw 2.146 3.120 nonbonded pdb=" NH1 ARG X 30 " pdb=" OE1 GLN X 114 " model vdw 2.166 3.120 nonbonded pdb=" O ILE 2 10 " pdb=" OG SER 2 14 " model vdw 2.170 3.040 ... (remaining 166597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20387 Z= 0.224 Angle : 0.732 25.001 27629 Z= 0.368 Chirality : 0.042 0.268 3178 Planarity : 0.005 0.115 3396 Dihedral : 14.424 178.146 7418 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2413 helix: 1.43 (0.13), residues: 1549 sheet: -1.27 (0.62), residues: 70 loop : -0.65 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 30 TYR 0.020 0.001 TYR 2 157 PHE 0.036 0.001 PHE L 26 TRP 0.056 0.002 TRP C 804 HIS 0.006 0.001 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (20381) covalent geometry : angle 0.73144 / 0.37 (27617) SS BOND : bond 0.00572 / 0.27 ( 6) SS BOND : angle 0.96510 / 0.48 ( 12) hydrogen bonds : bond 0.16631 / 11.30 ( 1232) hydrogen bonds : angle 5.86686 / 4.18 ( 3591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 603 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 ASP cc_start: 0.4954 (m-30) cc_final: 0.4527 (m-30) REVERT: U 13 GLU cc_start: 0.6464 (tt0) cc_final: 0.5517 (tt0) REVERT: U 143 PHE cc_start: 0.6303 (p90) cc_final: 0.5924 (p90) REVERT: U 144 LEU cc_start: 0.7778 (mt) cc_final: 0.7450 (mt) REVERT: W 43 TYR cc_start: 0.7405 (t80) cc_final: 0.7068 (t80) REVERT: X 19 TYR cc_start: 0.6414 (m-80) cc_final: 0.6140 (m-10) REVERT: X 107 GLU cc_start: 0.7125 (mp0) cc_final: 0.6481 (mp0) REVERT: X 109 LYS cc_start: 0.7600 (tppt) cc_final: 0.6995 (mtmt) REVERT: X 112 GLU cc_start: 0.6711 (tt0) cc_final: 0.6497 (tm-30) REVERT: X 124 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8015 (mm-30) REVERT: 1 30 LEU cc_start: 0.7058 (mt) cc_final: 0.6782 (mt) REVERT: 1 139 SER cc_start: 0.8359 (t) cc_final: 0.8137 (t) REVERT: 2 188 ASP cc_start: 0.6135 (m-30) cc_final: 0.5793 (t70) REVERT: 6 137 ASP cc_start: 0.7605 (p0) cc_final: 0.7383 (p0) REVERT: b 36 TYR cc_start: 0.7828 (m-80) cc_final: 0.7254 (m-80) REVERT: C 801 PRO cc_start: 0.6843 (Cg_endo) cc_final: 0.6521 (Cg_exo) REVERT: C 804 TRP cc_start: 0.7246 (t60) cc_final: 0.6831 (t60) REVERT: A 175 THR cc_start: 0.7804 (p) cc_final: 0.7034 (t) outliers start: 2 outliers final: 0 residues processed: 605 average time/residue: 0.1657 time to fit residues: 150.0387 Evaluate side-chains 306 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 HIS U 119 ASN 1 69 ASN 1 310 ASN 2 29 ASN 3 53 ASN 3 85 ASN 3 107 ASN 9 40 ASN C 704 ASN A 88 GLN A 165 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121447 restraints weight = 29218.160| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.14 r_work: 0.3507 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20387 Z= 0.150 Angle : 0.632 15.833 27629 Z= 0.325 Chirality : 0.041 0.253 3178 Planarity : 0.005 0.077 3396 Dihedral : 10.008 153.572 2866 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 2.34 % Allowed : 10.02 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 2413 helix: 1.71 (0.13), residues: 1564 sheet: -1.10 (0.61), residues: 77 loop : -0.62 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 618 TYR 0.025 0.001 TYR 1 244 PHE 0.026 0.002 PHE C 599 TRP 0.032 0.001 TRP C 804 HIS 0.011 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (20381) covalent geometry : angle 0.62360 / 0.32 (27617) SS BOND : bond 0.00689 / 0.32 ( 6) SS BOND : angle 4.92930 / 2.43 ( 12) hydrogen bonds : bond 0.04589 / 3.05 ( 1232) hydrogen bonds : angle 4.49552 / 3.24 ( 3591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8345 (ttp) REVERT: D 46 ASP cc_start: 0.7839 (m-30) cc_final: 0.7558 (m-30) REVERT: D 54 LEU cc_start: 0.6871 (mp) cc_final: 0.6647 (mp) REVERT: U 59 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: U 88 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8446 (ttpt) REVERT: W 45 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7335 (t80) REVERT: W 88 GLN cc_start: 0.7680 (tp40) cc_final: 0.7158 (tt0) REVERT: X 19 TYR cc_start: 0.7218 (m-80) cc_final: 0.6842 (m-10) REVERT: X 109 LYS cc_start: 0.7972 (tppt) cc_final: 0.7640 (mtmt) REVERT: X 124 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8258 (mm-30) REVERT: 1 290 MET cc_start: 0.7427 (mmm) cc_final: 0.7167 (mpp) REVERT: 2 152 LYS cc_start: 0.8396 (pttt) cc_final: 0.7900 (mttm) REVERT: 2 179 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8676 (mt) REVERT: 6 90 ASN cc_start: 0.7512 (p0) cc_final: 0.6902 (p0) REVERT: g 30 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.7071 (t80) REVERT: g 50 TYR cc_start: 0.6394 (m-10) cc_final: 0.6020 (m-10) REVERT: b 36 TYR cc_start: 0.7884 (m-80) cc_final: 0.7195 (m-80) REVERT: b 57 SER cc_start: 0.8110 (t) cc_final: 0.7711 (t) REVERT: C 533 PHE cc_start: 0.7535 (t80) cc_final: 0.7144 (t80) REVERT: C 554 PRO cc_start: 0.6429 (Cg_endo) cc_final: 0.6179 (Cg_exo) REVERT: C 570 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6356 (tm-30) REVERT: C 804 TRP cc_start: 0.7501 (t60) cc_final: 0.7261 (t60) REVERT: C 815 SER cc_start: 0.8667 (p) cc_final: 0.8313 (t) REVERT: C 838 MET cc_start: 0.8608 (tpt) cc_final: 0.8361 (tpt) REVERT: A 73 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6829 (mtpp) REVERT: A 74 MET cc_start: 0.7788 (ptt) cc_final: 0.7534 (ptt) REVERT: A 84 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7942 (mtm180) REVERT: A 153 ASP cc_start: 0.7849 (t0) cc_final: 0.7601 (t0) REVERT: A 163 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8264 (mm-40) REVERT: A 194 TYR cc_start: 0.8179 (p90) cc_final: 0.7760 (p90) REVERT: A 206 LYS cc_start: 0.7940 (mttp) cc_final: 0.7719 (mttp) outliers start: 50 outliers final: 21 residues processed: 343 average time/residue: 0.1463 time to fit residues: 78.5498 Evaluate side-chains 296 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 45 PHE Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 70 MET Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 2 residue 29 ASN Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 88 LYS Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 15 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 26 GLN U 8 HIS X 145 HIS ** b 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.142753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105665 restraints weight = 29443.261| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.40 r_work: 0.3246 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20387 Z= 0.192 Angle : 0.653 9.147 27629 Z= 0.335 Chirality : 0.043 0.170 3178 Planarity : 0.005 0.068 3396 Dihedral : 9.510 157.596 2866 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 2.11 % Allowed : 13.26 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2413 helix: 1.66 (0.13), residues: 1574 sheet: -0.92 (0.56), residues: 85 loop : -0.68 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 297 TYR 0.024 0.002 TYR A 117 PHE 0.032 0.002 PHE C 530 TRP 0.042 0.002 TRP U 149 HIS 0.006 0.001 HIS X 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (20381) covalent geometry : angle 0.65252 / 0.33 (27617) SS BOND : bond 0.00875 / 0.47 ( 6) SS BOND : angle 1.82128 / 1.01 ( 12) hydrogen bonds : bond 0.04839 / 3.23 ( 1232) hydrogen bonds : angle 4.30541 / 3.12 ( 3591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.8031 (m-30) cc_final: 0.7325 (m-30) REVERT: W 88 GLN cc_start: 0.7999 (tp40) cc_final: 0.7276 (tt0) REVERT: X 19 TYR cc_start: 0.8173 (m-80) cc_final: 0.7961 (m-80) REVERT: X 109 LYS cc_start: 0.8208 (tppt) cc_final: 0.7755 (mtmt) REVERT: X 124 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8043 (mm-30) REVERT: 1 21 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5219 (t80) REVERT: 1 273 PHE cc_start: 0.6691 (t80) cc_final: 0.6239 (m-80) REVERT: 1 288 PHE cc_start: 0.7322 (m-10) cc_final: 0.6954 (t80) REVERT: 1 290 MET cc_start: 0.7580 (mmm) cc_final: 0.7108 (mpp) REVERT: 2 15 MET cc_start: 0.8506 (mtm) cc_final: 0.8170 (ptp) REVERT: 2 63 SER cc_start: 0.8666 (p) cc_final: 0.8389 (p) REVERT: 2 152 LYS cc_start: 0.8423 (pttt) cc_final: 0.7767 (mttm) REVERT: 2 179 LEU cc_start: 0.9204 (mm) cc_final: 0.8970 (mt) REVERT: 2 184 LEU cc_start: 0.7820 (mm) cc_final: 0.7558 (mt) REVERT: 2 226 GLU cc_start: 0.8470 (tt0) cc_final: 0.8199 (tt0) REVERT: 6 90 ASN cc_start: 0.7385 (p0) cc_final: 0.6841 (p0) REVERT: g 30 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7176 (t80) REVERT: 9 40 ASN cc_start: 0.8566 (m110) cc_final: 0.8240 (m-40) REVERT: 9 42 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8397 (mm-30) REVERT: C 523 ARG cc_start: 0.7195 (tpt-90) cc_final: 0.6741 (tpp-160) REVERT: C 533 PHE cc_start: 0.7584 (t80) cc_final: 0.7341 (t80) REVERT: C 804 TRP cc_start: 0.7556 (t60) cc_final: 0.7243 (t60) REVERT: A 43 THR cc_start: 0.8530 (p) cc_final: 0.8327 (p) REVERT: A 84 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8435 (mtm180) REVERT: A 92 MET cc_start: 0.7573 (tpp) cc_final: 0.7199 (tpp) REVERT: A 153 ASP cc_start: 0.8355 (t0) cc_final: 0.7813 (t0) outliers start: 45 outliers final: 23 residues processed: 334 average time/residue: 0.1500 time to fit residues: 77.6216 Evaluate side-chains 283 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 88 LYS Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 135 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain g residue 32 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 139 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 199 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 106 HIS U 169 ASN 9 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107408 restraints weight = 29226.952| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.40 r_work: 0.3268 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20387 Z= 0.125 Angle : 0.556 9.701 27629 Z= 0.283 Chirality : 0.039 0.165 3178 Planarity : 0.004 0.062 3396 Dihedral : 9.091 156.993 2866 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 2.15 % Allowed : 15.74 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2413 helix: 1.91 (0.13), residues: 1576 sheet: -1.02 (0.57), residues: 83 loop : -0.61 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 49 TYR 0.020 0.001 TYR C 538 PHE 0.025 0.001 PHE C 530 TRP 0.021 0.001 TRP U 149 HIS 0.004 0.001 HIS g 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (20381) covalent geometry : angle 0.55450 / 0.28 (27617) SS BOND : bond 0.00807 / 0.60 ( 6) SS BOND : angle 1.73331 / 0.99 ( 12) hydrogen bonds : bond 0.03933 / 2.64 ( 1232) hydrogen bonds : angle 4.08972 / 2.97 ( 3591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.8331 (m-30) cc_final: 0.7598 (m-30) REVERT: U 18 MET cc_start: 0.7480 (tpp) cc_final: 0.7239 (tpt) REVERT: U 59 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: U 149 TRP cc_start: 0.7091 (m100) cc_final: 0.6179 (m100) REVERT: W 88 GLN cc_start: 0.8072 (tp40) cc_final: 0.7345 (tt0) REVERT: W 94 GLU cc_start: 0.8604 (tp30) cc_final: 0.8384 (tp30) REVERT: X 109 LYS cc_start: 0.8260 (tppt) cc_final: 0.7694 (mttt) REVERT: X 111 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7997 (t0) REVERT: X 115 MET cc_start: 0.7959 (mmt) cc_final: 0.7716 (mmt) REVERT: X 124 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7934 (mm-30) REVERT: 1 21 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.5194 (t80) REVERT: 1 86 ILE cc_start: 0.8385 (tt) cc_final: 0.7706 (pt) REVERT: 1 273 PHE cc_start: 0.6867 (t80) cc_final: 0.6360 (m-10) REVERT: 1 288 PHE cc_start: 0.7320 (m-10) cc_final: 0.6928 (t80) REVERT: 1 290 MET cc_start: 0.7623 (mmm) cc_final: 0.7298 (mpp) REVERT: 2 38 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8271 (mp) REVERT: 2 50 GLN cc_start: 0.8062 (tp40) cc_final: 0.7672 (mt0) REVERT: 2 57 GLU cc_start: 0.8763 (mp0) cc_final: 0.8531 (mp0) REVERT: 2 63 SER cc_start: 0.8590 (p) cc_final: 0.8289 (p) REVERT: 2 152 LYS cc_start: 0.8281 (pttt) cc_final: 0.7545 (mttm) REVERT: 2 179 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8952 (mt) REVERT: 2 190 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.5051 (tt) REVERT: 2 226 GLU cc_start: 0.8403 (tt0) cc_final: 0.8144 (tt0) REVERT: 2 433 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7809 (mt-10) REVERT: 3 67 ASP cc_start: 0.8741 (t0) cc_final: 0.8437 (t0) REVERT: 3 78 MET cc_start: 0.8382 (mmm) cc_final: 0.7975 (mmm) REVERT: 6 79 ASP cc_start: 0.8525 (t0) cc_final: 0.8323 (t0) REVERT: 6 90 ASN cc_start: 0.7429 (p0) cc_final: 0.6840 (p0) REVERT: g 30 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7428 (t80) REVERT: 9 46 GLU cc_start: 0.8143 (tp30) cc_final: 0.7873 (tp30) REVERT: C 523 ARG cc_start: 0.7255 (tpt-90) cc_final: 0.6830 (tpp-160) REVERT: C 533 PHE cc_start: 0.7360 (t80) cc_final: 0.7075 (t80) REVERT: C 534 MET cc_start: 0.7109 (mpp) cc_final: 0.6163 (mpp) REVERT: A 84 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8487 (mtm180) REVERT: A 92 MET cc_start: 0.7261 (tpp) cc_final: 0.7013 (tpp) REVERT: A 153 ASP cc_start: 0.8551 (t0) cc_final: 0.7954 (t0) REVERT: A 166 MET cc_start: 0.8917 (mtt) cc_final: 0.8695 (mtt) outliers start: 46 outliers final: 29 residues processed: 321 average time/residue: 0.1420 time to fit residues: 71.3886 Evaluate side-chains 299 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 93 LYS Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 190 LEU Chi-restraints excluded: chain 2 residue 254 SER Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain 9 residue 26 THR Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 115 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 197 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 169 ASN 2 29 ASN 9 40 ASN C 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105713 restraints weight = 29101.167| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.25 r_work: 0.3262 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20387 Z= 0.129 Angle : 0.551 8.149 27629 Z= 0.281 Chirality : 0.039 0.163 3178 Planarity : 0.004 0.059 3396 Dihedral : 8.774 156.692 2866 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 2.25 % Allowed : 16.49 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.18), residues: 2413 helix: 2.05 (0.13), residues: 1571 sheet: -0.89 (0.56), residues: 85 loop : -0.61 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 9 34 TYR 0.017 0.001 TYR 1 244 PHE 0.017 0.001 PHE U 123 TRP 0.019 0.001 TRP U 98 HIS 0.004 0.001 HIS g 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20381) covalent geometry : angle 0.54980 / 0.28 (27617) SS BOND : bond 0.00950 / 0.83 ( 6) SS BOND : angle 2.10539 / 1.04 ( 12) hydrogen bonds : bond 0.03891 / 2.62 ( 1232) hydrogen bonds : angle 3.99595 / 2.90 ( 3591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.8510 (m-30) cc_final: 0.7788 (m-30) REVERT: U 59 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: U 149 TRP cc_start: 0.7316 (m100) cc_final: 0.6915 (m100) REVERT: W 94 GLU cc_start: 0.8742 (tp30) cc_final: 0.8426 (tp30) REVERT: X 109 LYS cc_start: 0.8333 (tppt) cc_final: 0.7715 (mttt) REVERT: X 111 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8181 (t0) REVERT: X 112 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7037 (mt-10) REVERT: X 115 MET cc_start: 0.8111 (mmt) cc_final: 0.7860 (mmt) REVERT: X 124 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7944 (mm-30) REVERT: 1 21 TYR cc_start: 0.6201 (OUTLIER) cc_final: 0.5533 (t80) REVERT: 1 273 PHE cc_start: 0.7183 (t80) cc_final: 0.6639 (m-10) REVERT: 1 288 PHE cc_start: 0.7450 (m-10) cc_final: 0.7025 (t80) REVERT: 1 290 MET cc_start: 0.7973 (mmm) cc_final: 0.7502 (mpp) REVERT: 2 38 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8478 (mp) REVERT: 2 50 GLN cc_start: 0.8274 (tp40) cc_final: 0.7785 (mt0) REVERT: 2 57 GLU cc_start: 0.8909 (mp0) cc_final: 0.8644 (mp0) REVERT: 2 63 SER cc_start: 0.8701 (p) cc_final: 0.8408 (p) REVERT: 2 152 LYS cc_start: 0.8498 (pttt) cc_final: 0.7678 (mttm) REVERT: 2 179 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9007 (mt) REVERT: 2 226 GLU cc_start: 0.8672 (tt0) cc_final: 0.8444 (tt0) REVERT: 2 421 ILE cc_start: 0.9224 (pt) cc_final: 0.9009 (pt) REVERT: 3 78 MET cc_start: 0.8514 (mmm) cc_final: 0.8127 (mmm) REVERT: 6 27 LYS cc_start: 0.7291 (mptt) cc_final: 0.6824 (mmmt) REVERT: 6 90 ASN cc_start: 0.7280 (p0) cc_final: 0.6681 (p0) REVERT: g 30 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7435 (t80) REVERT: g 50 TYR cc_start: 0.7108 (m-10) cc_final: 0.6731 (m-10) REVERT: 9 42 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8591 (mm-30) REVERT: 9 46 GLU cc_start: 0.8276 (tp30) cc_final: 0.8065 (tp30) REVERT: C 534 MET cc_start: 0.7258 (mpp) cc_final: 0.6935 (mmt) REVERT: C 549 ASP cc_start: 0.7992 (t70) cc_final: 0.7682 (t0) REVERT: C 633 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8199 (mtt) REVERT: A 84 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8583 (mtm180) REVERT: A 92 MET cc_start: 0.7237 (tpp) cc_final: 0.6999 (tpp) REVERT: A 153 ASP cc_start: 0.8708 (t0) cc_final: 0.8133 (t0) outliers start: 48 outliers final: 28 residues processed: 301 average time/residue: 0.1389 time to fit residues: 65.9204 Evaluate side-chains 288 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 139 SER Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 254 SER Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 196 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 29 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 169 ASN 2 29 ASN 2 198 ASN b 22 ASN b 52 ASN 9 40 ASN C 537 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102783 restraints weight = 29106.693| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.27 r_work: 0.3210 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20387 Z= 0.161 Angle : 0.585 14.906 27629 Z= 0.294 Chirality : 0.040 0.165 3178 Planarity : 0.004 0.061 3396 Dihedral : 8.725 155.980 2866 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Rotamer: Outliers : 3.33 % Allowed : 16.16 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.17), residues: 2413 helix: 2.01 (0.13), residues: 1568 sheet: -0.68 (0.60), residues: 75 loop : -0.58 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 57 TYR 0.016 0.001 TYR 1 244 PHE 0.033 0.002 PHE C 533 TRP 0.020 0.001 TRP U 98 HIS 0.006 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (20381) covalent geometry : angle 0.58370 / 0.29 (27617) SS BOND : bond 0.00795 / 0.68 ( 6) SS BOND : angle 1.80291 / 0.96 ( 12) hydrogen bonds : bond 0.04130 / 2.77 ( 1232) hydrogen bonds : angle 4.04379 / 2.93 ( 3591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 275 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.8620 (m-30) cc_final: 0.7848 (m-30) REVERT: D 83 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6959 (tm-30) REVERT: U 59 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: U 149 TRP cc_start: 0.7737 (m100) cc_final: 0.7319 (m100) REVERT: W 94 GLU cc_start: 0.8792 (tp30) cc_final: 0.8518 (tp30) REVERT: X 109 LYS cc_start: 0.8468 (tppt) cc_final: 0.7869 (mttt) REVERT: X 111 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8378 (t0) REVERT: X 115 MET cc_start: 0.8119 (mmt) cc_final: 0.7899 (mmt) REVERT: X 124 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7929 (mm-30) REVERT: 1 21 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.5828 (t80) REVERT: 1 273 PHE cc_start: 0.7426 (t80) cc_final: 0.6732 (m-10) REVERT: 1 288 PHE cc_start: 0.7557 (m-10) cc_final: 0.7154 (t80) REVERT: 1 290 MET cc_start: 0.8017 (mmm) cc_final: 0.7552 (mpp) REVERT: 2 38 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (mp) REVERT: 2 50 GLN cc_start: 0.8421 (tp40) cc_final: 0.7852 (mt0) REVERT: 2 63 SER cc_start: 0.8806 (p) cc_final: 0.8564 (p) REVERT: 2 152 LYS cc_start: 0.8542 (pttt) cc_final: 0.7823 (mttm) REVERT: 2 421 ILE cc_start: 0.9164 (pt) cc_final: 0.8917 (pt) REVERT: 3 78 MET cc_start: 0.8566 (mmm) cc_final: 0.8276 (mmm) REVERT: 3 83 VAL cc_start: 0.8663 (m) cc_final: 0.8462 (m) REVERT: 6 27 LYS cc_start: 0.7617 (mptt) cc_final: 0.7082 (mmmt) REVERT: 6 30 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7865 (tmm) REVERT: 6 90 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.6855 (p0) REVERT: g 30 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7423 (t80) REVERT: g 50 TYR cc_start: 0.7339 (m-10) cc_final: 0.6969 (m-10) REVERT: g 60 GLN cc_start: 0.8381 (mt0) cc_final: 0.8057 (tt0) REVERT: 9 46 GLU cc_start: 0.8354 (tp30) cc_final: 0.8085 (tp30) REVERT: C 531 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4977 (m-80) REVERT: C 534 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6940 (mmt) REVERT: C 549 ASP cc_start: 0.8123 (t70) cc_final: 0.7795 (t0) REVERT: C 633 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8146 (mtm) REVERT: C 804 TRP cc_start: 0.7397 (t60) cc_final: 0.6942 (t60) REVERT: A 70 LYS cc_start: 0.8199 (tptt) cc_final: 0.7693 (ptmt) REVERT: A 84 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8696 (mtm180) REVERT: A 92 MET cc_start: 0.7206 (tpp) cc_final: 0.6939 (tpp) REVERT: A 153 ASP cc_start: 0.8798 (t0) cc_final: 0.8287 (t0) REVERT: A 159 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8289 (mptt) outliers start: 71 outliers final: 40 residues processed: 324 average time/residue: 0.1384 time to fit residues: 70.7841 Evaluate side-chains 310 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain X residue 111 ASP Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 236 ILE Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 29 ASN Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 254 SER Chi-restraints excluded: chain 2 residue 337 ILE Chi-restraints excluded: chain 2 residue 388 MET Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 38 LEU Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 179 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 ASN U 169 ASN b 52 ASN C 616 GLN A 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104538 restraints weight = 29397.228| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.35 r_work: 0.3231 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20387 Z= 0.116 Angle : 0.544 13.356 27629 Z= 0.276 Chirality : 0.038 0.158 3178 Planarity : 0.004 0.061 3396 Dihedral : 8.534 155.814 2866 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.94 % Favored : 95.94 % Rotamer: Outliers : 2.53 % Allowed : 17.10 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.18), residues: 2413 helix: 2.15 (0.13), residues: 1573 sheet: -0.68 (0.59), residues: 77 loop : -0.57 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 57 TYR 0.020 0.001 TYR 2 336 PHE 0.014 0.001 PHE 3 94 TRP 0.021 0.001 TRP U 98 HIS 0.004 0.001 HIS 2 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20381) covalent geometry : angle 0.53913 / 0.27 (27617) SS BOND : bond 0.00610 / 0.44 ( 6) SS BOND : angle 3.40785 / 1.67 ( 12) hydrogen bonds : bond 0.03772 / 2.54 ( 1232) hydrogen bonds : angle 3.94561 / 2.86 ( 3591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6945 (tm-30) REVERT: L 37 ASN cc_start: 0.8777 (t0) cc_final: 0.8391 (t0) REVERT: U 59 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: U 149 TRP cc_start: 0.7879 (m100) cc_final: 0.7226 (m100) REVERT: W 94 GLU cc_start: 0.8788 (tp30) cc_final: 0.8551 (tp30) REVERT: X 109 LYS cc_start: 0.8472 (tppt) cc_final: 0.7890 (mttt) REVERT: X 115 MET cc_start: 0.8097 (mmt) cc_final: 0.7897 (mmt) REVERT: X 124 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7913 (mm-30) REVERT: 1 273 PHE cc_start: 0.7499 (t80) cc_final: 0.6812 (m-10) REVERT: 1 288 PHE cc_start: 0.7476 (m-10) cc_final: 0.7119 (t80) REVERT: 1 290 MET cc_start: 0.8120 (mmm) cc_final: 0.7653 (mpp) REVERT: 2 38 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (mp) REVERT: 2 50 GLN cc_start: 0.8394 (tp40) cc_final: 0.7778 (mt0) REVERT: 2 57 GLU cc_start: 0.8924 (mp0) cc_final: 0.8604 (mp0) REVERT: 2 421 ILE cc_start: 0.9110 (pt) cc_final: 0.8885 (pt) REVERT: 3 78 MET cc_start: 0.8475 (mmm) cc_final: 0.8167 (mmm) REVERT: 3 83 VAL cc_start: 0.8660 (m) cc_final: 0.8443 (m) REVERT: 3 107 ASN cc_start: 0.8587 (m-40) cc_final: 0.8250 (m-40) REVERT: 6 27 LYS cc_start: 0.7644 (mptt) cc_final: 0.7107 (mmmt) REVERT: 6 30 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7797 (tmm) REVERT: 6 90 ASN cc_start: 0.7353 (p0) cc_final: 0.6811 (p0) REVERT: g 30 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7421 (t80) REVERT: g 50 TYR cc_start: 0.7347 (m-10) cc_final: 0.6968 (m-10) REVERT: g 60 GLN cc_start: 0.8385 (mt0) cc_final: 0.8038 (tt0) REVERT: 9 25 CYS cc_start: 0.6566 (t) cc_final: 0.6192 (t) REVERT: 9 42 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8642 (mm-30) REVERT: 9 46 GLU cc_start: 0.8287 (tp30) cc_final: 0.8034 (tp30) REVERT: C 523 ARG cc_start: 0.7268 (tpt-90) cc_final: 0.6795 (tpp80) REVERT: C 531 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5086 (m-80) REVERT: C 534 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7110 (mmt) REVERT: C 633 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: A 70 LYS cc_start: 0.8143 (tptt) cc_final: 0.7635 (ptmt) REVERT: A 84 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8699 (mtm110) REVERT: A 92 MET cc_start: 0.7217 (tpp) cc_final: 0.6941 (tpp) REVERT: A 153 ASP cc_start: 0.8801 (t0) cc_final: 0.8265 (t0) REVERT: A 159 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8241 (mptt) outliers start: 54 outliers final: 31 residues processed: 306 average time/residue: 0.1422 time to fit residues: 67.8827 Evaluate side-chains 296 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 423 ASP Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain C residue 531 TYR Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 165 ASN 2 29 ASN b 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098857 restraints weight = 29418.325| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.27 r_work: 0.3150 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 20387 Z= 0.221 Angle : 0.649 13.940 27629 Z= 0.328 Chirality : 0.042 0.184 3178 Planarity : 0.004 0.067 3396 Dihedral : 8.807 155.601 2866 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 2.53 % Allowed : 17.38 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2413 helix: 1.87 (0.13), residues: 1575 sheet: -0.75 (0.63), residues: 66 loop : -0.61 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 553 TYR 0.020 0.002 TYR 2 336 PHE 0.032 0.002 PHE g 8 TRP 0.029 0.002 TRP C 804 HIS 0.006 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (20381) covalent geometry : angle 0.64330 / 0.33 (27617) SS BOND : bond 0.00438 / 0.27 ( 6) SS BOND : angle 4.24555 / 1.78 ( 12) hydrogen bonds : bond 0.04618 / 3.09 ( 1232) hydrogen bonds : angle 4.12347 / 2.99 ( 3591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 83 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7013 (tm-30) REVERT: W 33 TYR cc_start: 0.4689 (m-80) cc_final: 0.4209 (p90) REVERT: X 109 LYS cc_start: 0.8321 (tppt) cc_final: 0.7774 (mttt) REVERT: X 115 MET cc_start: 0.8225 (mmt) cc_final: 0.8017 (mmt) REVERT: 1 21 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6284 (t80) REVERT: 1 273 PHE cc_start: 0.7692 (t80) cc_final: 0.6912 (m-10) REVERT: 1 288 PHE cc_start: 0.7556 (m-10) cc_final: 0.7102 (t80) REVERT: 1 290 MET cc_start: 0.8151 (mmm) cc_final: 0.7696 (mpp) REVERT: 2 38 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8631 (mp) REVERT: 2 50 GLN cc_start: 0.8501 (tp40) cc_final: 0.7949 (mt0) REVERT: 2 433 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8163 (mm-30) REVERT: 3 78 MET cc_start: 0.8663 (mmm) cc_final: 0.8093 (mmm) REVERT: 3 83 VAL cc_start: 0.8739 (m) cc_final: 0.8539 (m) REVERT: 3 107 ASN cc_start: 0.8675 (m-40) cc_final: 0.8354 (m-40) REVERT: 6 27 LYS cc_start: 0.7905 (mptt) cc_final: 0.7296 (mmmt) REVERT: 6 30 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: 6 90 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6796 (p0) REVERT: g 60 GLN cc_start: 0.8456 (mt0) cc_final: 0.8150 (tt0) REVERT: 9 34 ARG cc_start: 0.5957 (tpp-160) cc_final: 0.5393 (mmt90) REVERT: 9 46 GLU cc_start: 0.8399 (tp30) cc_final: 0.8110 (tp30) REVERT: C 523 ARG cc_start: 0.7276 (tpt-90) cc_final: 0.6815 (tpp80) REVERT: C 534 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7108 (mmt) REVERT: C 633 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8202 (mtm) REVERT: C 723 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.5158 (mtt180) REVERT: C 842 MET cc_start: 0.8111 (mmm) cc_final: 0.7877 (mmm) REVERT: A 70 LYS cc_start: 0.8124 (tptt) cc_final: 0.7633 (ptmt) REVERT: A 84 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8746 (mtm180) REVERT: A 92 MET cc_start: 0.7526 (tpp) cc_final: 0.7262 (tpp) REVERT: A 153 ASP cc_start: 0.8858 (t0) cc_final: 0.8314 (t0) REVERT: A 163 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8585 (mm-40) outliers start: 54 outliers final: 35 residues processed: 311 average time/residue: 0.1439 time to fit residues: 69.9237 Evaluate side-chains 298 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 29 ASN Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 116 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 427 ILE Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 107 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 0.0670 chunk 202 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 210 optimal weight: 0.4980 chunk 200 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 127 ASN 1 165 ASN b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102816 restraints weight = 28936.838| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.26 r_work: 0.3209 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20387 Z= 0.119 Angle : 0.568 13.615 27629 Z= 0.287 Chirality : 0.039 0.290 3178 Planarity : 0.004 0.064 3396 Dihedral : 8.562 154.974 2866 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 2.06 % Allowed : 17.99 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.18), residues: 2413 helix: 2.10 (0.13), residues: 1570 sheet: -0.77 (0.63), residues: 69 loop : -0.54 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 42 TYR 0.022 0.001 TYR C 538 PHE 0.027 0.001 PHE g 8 TRP 0.022 0.001 TRP C 795 HIS 0.003 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (20381) covalent geometry : angle 0.56395 / 0.29 (27617) SS BOND : bond 0.00127 / 0.09 ( 6) SS BOND : angle 3.25813 / 1.33 ( 12) hydrogen bonds : bond 0.03902 / 2.63 ( 1232) hydrogen bonds : angle 3.97559 / 2.88 ( 3591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: W 33 TYR cc_start: 0.4689 (m-80) cc_final: 0.4208 (p90) REVERT: W 78 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8175 (t0) REVERT: W 94 GLU cc_start: 0.8699 (tp30) cc_final: 0.8439 (tp30) REVERT: X 109 LYS cc_start: 0.8276 (tppt) cc_final: 0.7779 (mttt) REVERT: X 115 MET cc_start: 0.8210 (mmt) cc_final: 0.8001 (mmt) REVERT: 1 21 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.6127 (t80) REVERT: 1 273 PHE cc_start: 0.7679 (t80) cc_final: 0.6921 (m-10) REVERT: 1 288 PHE cc_start: 0.7459 (m-10) cc_final: 0.7004 (t80) REVERT: 1 290 MET cc_start: 0.8147 (mmm) cc_final: 0.7637 (mpp) REVERT: 2 38 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8620 (mp) REVERT: 2 50 GLN cc_start: 0.8409 (tp40) cc_final: 0.7820 (mt0) REVERT: 2 57 GLU cc_start: 0.8909 (mp0) cc_final: 0.8556 (mp0) REVERT: 2 421 ILE cc_start: 0.9043 (pt) cc_final: 0.8776 (pt) REVERT: 3 22 ASN cc_start: 0.7007 (m-40) cc_final: 0.6777 (m110) REVERT: 3 78 MET cc_start: 0.8486 (mmm) cc_final: 0.7920 (mmm) REVERT: 3 83 VAL cc_start: 0.8681 (m) cc_final: 0.8474 (m) REVERT: 6 27 LYS cc_start: 0.7803 (mptt) cc_final: 0.7315 (mmtt) REVERT: 6 30 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7771 (tmm) REVERT: 6 90 ASN cc_start: 0.7267 (p0) cc_final: 0.6717 (p0) REVERT: g 50 TYR cc_start: 0.7446 (m-10) cc_final: 0.7140 (m-10) REVERT: g 60 GLN cc_start: 0.8410 (mt0) cc_final: 0.8168 (tt0) REVERT: b 62 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6408 (tt0) REVERT: 9 34 ARG cc_start: 0.6033 (tpp-160) cc_final: 0.5678 (mmt90) REVERT: 9 46 GLU cc_start: 0.8288 (tp30) cc_final: 0.8033 (tp30) REVERT: C 523 ARG cc_start: 0.7279 (tpt-90) cc_final: 0.6811 (tpp80) REVERT: C 534 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7013 (mmt) REVERT: C 633 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8181 (mtm) REVERT: C 842 MET cc_start: 0.8075 (mmm) cc_final: 0.7849 (mmm) REVERT: A 70 LYS cc_start: 0.8017 (tptt) cc_final: 0.7587 (ptmt) REVERT: A 84 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8699 (mtm180) REVERT: A 92 MET cc_start: 0.7381 (tpp) cc_final: 0.7130 (tpp) REVERT: A 153 ASP cc_start: 0.8823 (t0) cc_final: 0.8339 (t0) outliers start: 44 outliers final: 29 residues processed: 305 average time/residue: 0.1432 time to fit residues: 68.6032 Evaluate side-chains 303 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 82 LEU Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 795 TRP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 127 ASN ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102390 restraints weight = 29330.390| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.27 r_work: 0.3201 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20387 Z= 0.136 Angle : 0.585 13.584 27629 Z= 0.294 Chirality : 0.039 0.217 3178 Planarity : 0.004 0.063 3396 Dihedral : 8.434 154.194 2866 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 2.11 % Allowed : 17.75 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.18), residues: 2413 helix: 2.11 (0.13), residues: 1574 sheet: -0.69 (0.63), residues: 68 loop : -0.54 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 42 TYR 0.023 0.001 TYR 2 336 PHE 0.029 0.001 PHE 1 224 TRP 0.021 0.002 TRP U 98 HIS 0.003 0.001 HIS b 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (20381) covalent geometry : angle 0.57931 / 0.29 (27617) SS BOND : bond 0.00110 / 0.09 ( 6) SS BOND : angle 4.08323 / 1.78 ( 12) hydrogen bonds : bond 0.03935 / 2.64 ( 1232) hydrogen bonds : angle 3.95839 / 2.87 ( 3591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 33 TYR cc_start: 0.4523 (m-80) cc_final: 0.3992 (p90) REVERT: W 78 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8126 (t0) REVERT: W 94 GLU cc_start: 0.8721 (tp30) cc_final: 0.8457 (tp30) REVERT: X 109 LYS cc_start: 0.8331 (tppt) cc_final: 0.7815 (mttt) REVERT: X 115 MET cc_start: 0.8275 (mmt) cc_final: 0.8057 (mmt) REVERT: 1 228 PHE cc_start: 0.6341 (t80) cc_final: 0.6097 (t80) REVERT: 1 273 PHE cc_start: 0.7705 (t80) cc_final: 0.6940 (m-10) REVERT: 1 288 PHE cc_start: 0.7481 (m-10) cc_final: 0.7056 (t80) REVERT: 1 290 MET cc_start: 0.8148 (mmm) cc_final: 0.7701 (mpp) REVERT: 2 38 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8605 (mp) REVERT: 2 50 GLN cc_start: 0.8440 (tp40) cc_final: 0.7836 (mt0) REVERT: 2 57 GLU cc_start: 0.8920 (mp0) cc_final: 0.8567 (mp0) REVERT: 2 421 ILE cc_start: 0.9044 (pt) cc_final: 0.8766 (pt) REVERT: 2 427 ILE cc_start: 0.8587 (tp) cc_final: 0.8297 (pt) REVERT: 3 22 ASN cc_start: 0.6984 (m-40) cc_final: 0.6745 (m110) REVERT: 3 78 MET cc_start: 0.8523 (mmm) cc_final: 0.7947 (mmm) REVERT: 3 83 VAL cc_start: 0.8592 (m) cc_final: 0.8351 (m) REVERT: 6 27 LYS cc_start: 0.7841 (mptt) cc_final: 0.7345 (mmtt) REVERT: 6 30 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7755 (tmm) REVERT: 6 90 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6745 (p0) REVERT: g 50 TYR cc_start: 0.7373 (m-10) cc_final: 0.7051 (m-10) REVERT: b 62 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6558 (tt0) REVERT: 9 25 CYS cc_start: 0.6010 (t) cc_final: 0.5552 (t) REVERT: 9 46 GLU cc_start: 0.8278 (tp30) cc_final: 0.8022 (tp30) REVERT: C 523 ARG cc_start: 0.7273 (tpt-90) cc_final: 0.6812 (tpp80) REVERT: C 534 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7006 (mmt) REVERT: C 633 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: C 842 MET cc_start: 0.8069 (mmm) cc_final: 0.7864 (mmm) REVERT: A 70 LYS cc_start: 0.8023 (tptt) cc_final: 0.7738 (tptp) REVERT: A 84 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (mtm180) REVERT: A 92 MET cc_start: 0.7393 (tpp) cc_final: 0.7113 (tpp) REVERT: A 153 ASP cc_start: 0.8839 (t0) cc_final: 0.8348 (t0) outliers start: 45 outliers final: 34 residues processed: 312 average time/residue: 0.1439 time to fit residues: 70.2978 Evaluate side-chains 312 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain 1 residue 89 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 1 residue 152 SER Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 28 ILE Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain 6 residue 102 ILE Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 817 CYS Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 48 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 215 optimal weight: 0.0670 chunk 52 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 0.0060 chunk 155 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103942 restraints weight = 29146.284| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.29 r_work: 0.3226 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20387 Z= 0.117 Angle : 0.567 13.043 27629 Z= 0.286 Chirality : 0.039 0.226 3178 Planarity : 0.004 0.063 3396 Dihedral : 8.299 153.119 2866 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 1.87 % Allowed : 18.08 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.18), residues: 2413 helix: 2.22 (0.13), residues: 1567 sheet: -0.97 (0.63), residues: 65 loop : -0.55 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 76 TYR 0.020 0.001 TYR 2 336 PHE 0.026 0.001 PHE 1 224 TRP 0.030 0.001 TRP C 795 HIS 0.004 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (20381) covalent geometry : angle 0.56069 / 0.28 (27617) SS BOND : bond 0.00082 / 0.06 ( 6) SS BOND : angle 4.10665 / 1.83 ( 12) hydrogen bonds : bond 0.03686 / 2.47 ( 1232) hydrogen bonds : angle 3.89794 / 2.82 ( 3591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5264.96 seconds wall clock time: 90 minutes 57.39 seconds (5457.39 seconds total)