Starting phenix.real_space_refine on Thu Mar 5 09:38:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zkp_14764/03_2026/7zkp_14764.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zkp_14764/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zkp_14764/03_2026/7zkp_14764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zkp_14764/03_2026/7zkp_14764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zkp_14764/03_2026/7zkp_14764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zkp_14764/03_2026/7zkp_14764.map" } 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-5986/lib/python3.9/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: 4.67, per 1000 atoms: 0.23 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: 1.58 Conformation dependent library (CDL) restraints added in 932.9 milliseconds 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: 0.43 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: 3.19 Time building geometry restraints manager: 2.10 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: 11876 35.63 - 71.26: 275 71.26 - 106.89: 22 106.89 - 142.52: 3 142.52 - 178.15: 3 Dihedral angle restraints: 12179 sinusoidal: 4981 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 12176 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.140 Find NCS groups from input model: 0.110 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 15.303 178.146 7531 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 covalent geometry : bond 0.00438 (20381) covalent geometry : angle 0.73144 (27617) SS BOND : bond 0.00572 ( 6) SS BOND : angle 0.96510 ( 12) hydrogen bonds : bond 0.16631 ( 1232) hydrogen bonds : angle 5.86686 ( 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 : 0.660 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: 0.1545 time to fit residues: 139.1060 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 : 0.645 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 76 HIS U 119 ASN 1 69 ASN 1 310 ASN 2 29 ASN 3 53 ASN 3 85 ASN 3 107 ASN ** b 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN A 88 GLN A 165 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.154130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121230 restraints weight = 29223.946| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.15 r_work: 0.3508 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 20387 Z= 0.159 Angle : 0.635 15.319 27629 Z= 0.326 Chirality : 0.041 0.266 3178 Planarity : 0.005 0.077 3396 Dihedral : 12.389 152.906 2979 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.57 % Rotamer: Outliers : 2.34 % Allowed : 10.21 % Favored : 87.45 % 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: 1563 sheet: -1.10 (0.61), residues: 77 loop : -0.63 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 618 TYR 0.025 0.001 TYR 1 244 PHE 0.026 0.002 PHE C 599 TRP 0.034 0.001 TRP C 804 HIS 0.013 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00332 (20381) covalent geometry : angle 0.62734 (27617) SS BOND : bond 0.00510 ( 6) SS BOND : angle 4.79397 ( 12) hydrogen bonds : bond 0.04540 ( 1232) hydrogen bonds : angle 4.48902 ( 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 368 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8339 (ttp) REVERT: D 46 ASP cc_start: 0.7844 (m-30) cc_final: 0.7564 (m-30) REVERT: D 54 LEU cc_start: 0.6859 (mp) cc_final: 0.6638 (mp) REVERT: U 59 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: U 88 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8446 (ttpt) REVERT: W 45 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7337 (t80) REVERT: W 88 GLN cc_start: 0.7693 (tp40) cc_final: 0.7166 (tt0) REVERT: X 19 TYR cc_start: 0.7228 (m-80) cc_final: 0.6848 (m-10) REVERT: X 109 LYS cc_start: 0.7968 (tppt) cc_final: 0.7640 (mtmt) REVERT: X 124 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8266 (mm-30) REVERT: 1 290 MET cc_start: 0.7447 (mmm) cc_final: 0.7180 (mpp) REVERT: 2 152 LYS cc_start: 0.8407 (pttt) cc_final: 0.7906 (mttm) REVERT: 2 179 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8680 (mt) REVERT: 2 297 MET cc_start: 0.8977 (ttp) cc_final: 0.8777 (ttp) REVERT: 6 90 ASN cc_start: 0.7517 (p0) cc_final: 0.6907 (p0) REVERT: g 30 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7071 (t80) REVERT: g 50 TYR cc_start: 0.6380 (m-10) cc_final: 0.6023 (m-10) REVERT: b 36 TYR cc_start: 0.7889 (m-80) cc_final: 0.7202 (m-80) REVERT: b 57 SER cc_start: 0.8104 (t) cc_final: 0.7702 (t) REVERT: C 533 PHE cc_start: 0.7538 (t80) cc_final: 0.7191 (t80) REVERT: C 554 PRO cc_start: 0.6431 (Cg_endo) cc_final: 0.6182 (Cg_exo) REVERT: C 570 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: C 804 TRP cc_start: 0.7501 (t60) cc_final: 0.7252 (t60) REVERT: C 815 SER cc_start: 0.8665 (p) cc_final: 0.8309 (t) REVERT: C 838 MET cc_start: 0.8596 (tpt) cc_final: 0.8351 (tpt) REVERT: A 73 LYS cc_start: 0.7184 (mmtt) cc_final: 0.6818 (mtpp) REVERT: A 74 MET cc_start: 0.7785 (ptt) cc_final: 0.7532 (ptt) REVERT: A 84 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7935 (mtm180) REVERT: A 153 ASP cc_start: 0.7845 (t0) cc_final: 0.7592 (t0) REVERT: A 163 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 194 TYR cc_start: 0.8185 (p90) cc_final: 0.7755 (p90) REVERT: A 206 LYS cc_start: 0.7948 (mttp) cc_final: 0.7726 (mttp) outliers start: 50 outliers final: 23 residues processed: 345 average time/residue: 0.1405 time to fit residues: 75.9294 Evaluate side-chains 298 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 9 LEU 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 16 LEU 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: 1.9990 chunk 187 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN U 8 HIS b 22 ASN C 787 GLN A 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114962 restraints weight = 29672.873| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.22 r_work: 0.3402 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20387 Z= 0.149 Angle : 0.579 8.558 27629 Z= 0.297 Chirality : 0.040 0.162 3178 Planarity : 0.004 0.067 3396 Dihedral : 11.549 156.647 2979 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.90 % Rotamer: Outliers : 1.73 % Allowed : 12.97 % Favored : 85.29 % 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: 1.50 (0.18), residues: 2413 helix: 1.85 (0.13), residues: 1574 sheet: -0.85 (0.59), residues: 81 loop : -0.59 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 47 TYR 0.021 0.001 TYR A 117 PHE 0.027 0.002 PHE C 530 TRP 0.031 0.002 TRP U 149 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00342 (20381) covalent geometry : angle 0.57774 (27617) SS BOND : bond 0.00577 ( 6) SS BOND : angle 2.04208 ( 12) hydrogen bonds : bond 0.04269 ( 1232) hydrogen bonds : angle 4.23125 ( 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 322 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8583 (ttp) cc_final: 0.8377 (ttp) REVERT: D 46 ASP cc_start: 0.8192 (m-30) cc_final: 0.7716 (m-30) REVERT: L 17 PHE cc_start: 0.7780 (m-80) cc_final: 0.7565 (m-80) REVERT: U 88 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8482 (ttpt) REVERT: U 105 ASN cc_start: 0.8921 (t0) cc_final: 0.8679 (t0) REVERT: W 88 GLN cc_start: 0.7871 (tp40) cc_final: 0.7298 (tt0) REVERT: X 19 TYR cc_start: 0.7760 (m-80) cc_final: 0.7548 (m-10) REVERT: X 109 LYS cc_start: 0.8152 (tppt) cc_final: 0.7715 (mtmt) REVERT: X 115 MET cc_start: 0.7946 (mmt) cc_final: 0.7535 (mmt) REVERT: X 124 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8200 (mm-30) REVERT: 1 288 PHE cc_start: 0.7321 (m-10) cc_final: 0.7095 (t80) REVERT: 1 290 MET cc_start: 0.7836 (mmm) cc_final: 0.7371 (mpp) REVERT: 2 152 LYS cc_start: 0.8461 (pttt) cc_final: 0.7841 (mttm) REVERT: 6 90 ASN cc_start: 0.7349 (p0) cc_final: 0.6786 (p0) REVERT: g 30 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7238 (t80) REVERT: g 50 TYR cc_start: 0.6902 (m-10) cc_final: 0.6546 (m-10) REVERT: 9 46 GLU cc_start: 0.8275 (tp30) cc_final: 0.8012 (tp30) REVERT: C 523 ARG cc_start: 0.7244 (tpt-90) cc_final: 0.6812 (tpp-160) REVERT: C 533 PHE cc_start: 0.7608 (t80) cc_final: 0.7399 (t80) REVERT: C 554 PRO cc_start: 0.6612 (Cg_endo) cc_final: 0.6388 (Cg_exo) REVERT: C 804 TRP cc_start: 0.7553 (t60) cc_final: 0.7292 (t60) REVERT: A 73 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6980 (mtpt) REVERT: A 84 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8325 (mtm180) REVERT: A 92 MET cc_start: 0.7211 (tpp) cc_final: 0.6910 (tpp) REVERT: A 113 ASP cc_start: 0.8559 (p0) cc_final: 0.8340 (p0) REVERT: A 153 ASP cc_start: 0.8073 (t0) cc_final: 0.7516 (t0) REVERT: A 194 TYR cc_start: 0.8380 (p90) cc_final: 0.8166 (p90) outliers start: 37 outliers final: 20 residues processed: 312 average time/residue: 0.1398 time to fit residues: 67.7638 Evaluate side-chains 269 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 1 residue 296 VAL 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 105 THR Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 64 LEU Chi-restraints excluded: chain C residue 699 SER Chi-restraints excluded: chain C residue 719 HIS 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 189 ASN 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: 0.9980 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 190 optimal weight: 0.0970 chunk 199 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 106 HIS X 145 HIS b 22 ASN C 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107697 restraints weight = 29310.457| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.40 r_work: 0.3276 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20387 Z= 0.155 Angle : 0.584 9.337 27629 Z= 0.296 Chirality : 0.040 0.165 3178 Planarity : 0.004 0.059 3396 Dihedral : 10.972 156.759 2979 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 2.20 % Allowed : 14.61 % Favored : 83.19 % 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: 1.53 (0.17), residues: 2413 helix: 1.91 (0.13), residues: 1573 sheet: -1.12 (0.57), residues: 83 loop : -0.62 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG 9 34 TYR 0.022 0.001 TYR A 117 PHE 0.028 0.001 PHE C 530 TRP 0.023 0.001 TRP C 804 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00357 (20381) covalent geometry : angle 0.58330 (27617) SS BOND : bond 0.00580 ( 6) SS BOND : angle 1.85387 ( 12) hydrogen bonds : bond 0.04116 ( 1232) hydrogen bonds : angle 4.12470 ( 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 328 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.8226 (m-30) cc_final: 0.7535 (m-30) REVERT: U 59 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: W 88 GLN cc_start: 0.8003 (tp40) cc_final: 0.7262 (tt0) REVERT: W 94 GLU cc_start: 0.8611 (tp30) cc_final: 0.8201 (tp30) REVERT: X 109 LYS cc_start: 0.8197 (tppt) cc_final: 0.7788 (mtmt) REVERT: X 115 MET cc_start: 0.7920 (mmt) cc_final: 0.7554 (mmt) REVERT: X 124 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8004 (mm-30) REVERT: 1 12 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7191 (mt) REVERT: 1 21 TYR cc_start: 0.5762 (OUTLIER) cc_final: 0.5258 (t80) REVERT: 1 288 PHE cc_start: 0.7242 (m-10) cc_final: 0.6935 (t80) REVERT: 1 290 MET cc_start: 0.7585 (mmm) cc_final: 0.7292 (mpp) REVERT: 2 38 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8164 (mp) REVERT: 2 152 LYS cc_start: 0.8327 (pttt) cc_final: 0.7668 (mttm) REVERT: 2 179 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8897 (mt) REVERT: 2 421 ILE cc_start: 0.9188 (pt) cc_final: 0.8968 (pt) REVERT: 3 34 LYS cc_start: 0.7149 (mmtm) cc_final: 0.6922 (mmtm) REVERT: 3 67 ASP cc_start: 0.8721 (t0) cc_final: 0.8461 (t0) REVERT: 3 78 MET cc_start: 0.8280 (mmm) cc_final: 0.7927 (mmm) REVERT: 6 2 MET cc_start: 0.3502 (mmm) cc_final: 0.2982 (mmm) REVERT: 6 30 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7573 (tmm) REVERT: 6 90 ASN cc_start: 0.7394 (p0) cc_final: 0.6800 (p0) REVERT: g 30 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7252 (t80) REVERT: g 50 TYR cc_start: 0.6955 (m-10) cc_final: 0.6705 (m-10) REVERT: 9 12 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8356 (mtm180) REVERT: 9 42 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8436 (mm-30) REVERT: 9 46 GLU cc_start: 0.7990 (tp30) cc_final: 0.7684 (tp30) REVERT: C 523 ARG cc_start: 0.7331 (tpt-90) cc_final: 0.6895 (tpp-160) REVERT: C 534 MET cc_start: 0.7343 (mpp) cc_final: 0.7065 (mpp) REVERT: C 536 ARG cc_start: 0.6236 (mmt90) cc_final: 0.5721 (mtt180) REVERT: C 554 PRO cc_start: 0.6683 (Cg_endo) cc_final: 0.6466 (Cg_exo) REVERT: C 585 PHE cc_start: 0.5874 (m-10) cc_final: 0.5646 (m-80) REVERT: C 804 TRP cc_start: 0.7398 (t60) cc_final: 0.7159 (t60) REVERT: A 84 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8461 (mtm180) REVERT: A 92 MET cc_start: 0.7274 (tpp) cc_final: 0.6829 (tpp) REVERT: A 113 ASP cc_start: 0.8371 (p0) cc_final: 0.8073 (p0) REVERT: A 153 ASP cc_start: 0.8398 (t0) cc_final: 0.7777 (t0) REVERT: A 166 MET cc_start: 0.8810 (mtt) cc_final: 0.8600 (mtt) outliers start: 47 outliers final: 24 residues processed: 312 average time/residue: 0.1316 time to fit residues: 64.2960 Evaluate side-chains 284 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR 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 W residue 34 LEU Chi-restraints excluded: chain 1 residue 11 PHE Chi-restraints excluded: chain 1 residue 12 LEU 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 116 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 466 VAL Chi-restraints excluded: chain 6 residue 30 MET 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 g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain C residue 699 SER 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: 0.0030 chunk 173 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 143 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN 1 173 GLN 2 29 ASN C 522 GLN A 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109107 restraints weight = 28956.373| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.25 r_work: 0.3316 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20387 Z= 0.112 Angle : 0.532 8.235 27629 Z= 0.272 Chirality : 0.038 0.172 3178 Planarity : 0.004 0.054 3396 Dihedral : 10.284 157.299 2979 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 2.15 % Allowed : 16.53 % Favored : 81.31 % 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: 1.76 (0.18), residues: 2413 helix: 2.11 (0.13), residues: 1573 sheet: -1.07 (0.55), residues: 85 loop : -0.59 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 57 TYR 0.026 0.001 TYR A 194 PHE 0.026 0.001 PHE g 8 TRP 0.018 0.001 TRP C 804 HIS 0.003 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00243 (20381) covalent geometry : angle 0.52944 (27617) SS BOND : bond 0.01221 ( 6) SS BOND : angle 2.52251 ( 12) hydrogen bonds : bond 0.03695 ( 1232) hydrogen bonds : angle 3.97647 ( 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 324 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8484 (ttp) cc_final: 0.8265 (ttp) REVERT: D 46 ASP cc_start: 0.8404 (m-30) cc_final: 0.8193 (m-30) REVERT: U 59 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: W 88 GLN cc_start: 0.8116 (tp40) cc_final: 0.7358 (tt0) REVERT: W 94 GLU cc_start: 0.8665 (tp30) cc_final: 0.8201 (tp30) REVERT: X 19 TYR cc_start: 0.8369 (m-80) cc_final: 0.8090 (m-80) REVERT: X 109 LYS cc_start: 0.8290 (tppt) cc_final: 0.7833 (mtmt) REVERT: X 112 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6972 (tt0) REVERT: X 115 MET cc_start: 0.8010 (mmt) cc_final: 0.7615 (mmt) REVERT: X 124 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7924 (mm-30) REVERT: 1 21 TYR cc_start: 0.5880 (OUTLIER) cc_final: 0.5302 (t80) REVERT: 1 86 ILE cc_start: 0.8445 (tp) cc_final: 0.7867 (pt) REVERT: 1 273 PHE cc_start: 0.7049 (t80) cc_final: 0.6452 (m-10) REVERT: 1 288 PHE cc_start: 0.7398 (m-10) cc_final: 0.6965 (t80) REVERT: 1 290 MET cc_start: 0.7979 (mmm) cc_final: 0.7560 (mpp) REVERT: 2 57 GLU cc_start: 0.8804 (mp0) cc_final: 0.8596 (mp0) REVERT: 2 152 LYS cc_start: 0.8383 (pttt) cc_final: 0.7602 (mttm) REVERT: 2 179 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8957 (mt) REVERT: 3 67 ASP cc_start: 0.8798 (t0) cc_final: 0.8525 (t0) REVERT: 3 78 MET cc_start: 0.8288 (mmm) cc_final: 0.7979 (mmm) REVERT: 6 2 MET cc_start: 0.3494 (mmm) cc_final: 0.3015 (mmm) REVERT: 6 90 ASN cc_start: 0.7377 (p0) cc_final: 0.6778 (p0) REVERT: g 30 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7361 (t80) REVERT: g 50 TYR cc_start: 0.7155 (m-10) cc_final: 0.6781 (m-10) REVERT: 9 42 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8462 (mm-30) REVERT: 9 46 GLU cc_start: 0.8168 (tp30) cc_final: 0.7893 (tp30) REVERT: C 523 ARG cc_start: 0.7196 (tpt-90) cc_final: 0.6747 (tpp-160) REVERT: C 534 MET cc_start: 0.7273 (mpp) cc_final: 0.6955 (mmt) REVERT: C 633 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: A 84 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8548 (mtm180) REVERT: A 92 MET cc_start: 0.7310 (tpp) cc_final: 0.6916 (tpp) REVERT: A 113 ASP cc_start: 0.8100 (p0) cc_final: 0.7854 (p0) REVERT: A 153 ASP cc_start: 0.8605 (t0) cc_final: 0.7937 (t0) REVERT: A 166 MET cc_start: 0.8890 (mtt) cc_final: 0.8627 (mtt) outliers start: 46 outliers final: 24 residues processed: 309 average time/residue: 0.1391 time to fit residues: 67.2691 Evaluate side-chains 287 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 U residue 91 LEU Chi-restraints excluded: chain W residue 34 LEU 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 139 SER Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 3 residue 105 GLU Chi-restraints excluded: chain 6 residue 50 ILE Chi-restraints excluded: chain 6 residue 105 THR Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain C residue 633 MET 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 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 196 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 43 ASN U 169 ASN 2 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108044 restraints weight = 29085.146| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.34 r_work: 0.3296 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20387 Z= 0.120 Angle : 0.542 12.494 27629 Z= 0.272 Chirality : 0.038 0.168 3178 Planarity : 0.004 0.058 3396 Dihedral : 9.976 155.702 2979 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Rotamer: Outliers : 2.30 % Allowed : 17.28 % Favored : 80.42 % 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: 1.86 (0.18), residues: 2413 helix: 2.17 (0.13), residues: 1574 sheet: -0.87 (0.60), residues: 75 loop : -0.54 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 161 TYR 0.025 0.001 TYR A 194 PHE 0.014 0.001 PHE 3 94 TRP 0.015 0.001 TRP U 149 HIS 0.003 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00266 (20381) covalent geometry : angle 0.54125 (27617) SS BOND : bond 0.00402 ( 6) SS BOND : angle 1.65411 ( 12) hydrogen bonds : bond 0.03628 ( 1232) hydrogen bonds : angle 3.91425 ( 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 323 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8335 (ttp) cc_final: 0.8126 (ttp) REVERT: D 46 ASP cc_start: 0.8197 (m-30) cc_final: 0.7376 (m-30) REVERT: U 59 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: W 94 GLU cc_start: 0.8603 (tp30) cc_final: 0.8289 (tp30) REVERT: X 19 TYR cc_start: 0.8438 (m-80) cc_final: 0.8186 (m-80) REVERT: X 109 LYS cc_start: 0.8245 (tppt) cc_final: 0.7809 (mtmt) REVERT: X 115 MET cc_start: 0.8108 (mmt) cc_final: 0.7793 (mmt) REVERT: X 124 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7852 (mm-30) REVERT: 1 21 TYR cc_start: 0.5860 (OUTLIER) cc_final: 0.5213 (t80) REVERT: 1 86 ILE cc_start: 0.8481 (tp) cc_final: 0.7945 (pt) REVERT: 1 273 PHE cc_start: 0.6918 (t80) cc_final: 0.6542 (m-10) REVERT: 1 288 PHE cc_start: 0.7239 (m-10) cc_final: 0.6924 (t80) REVERT: 1 290 MET cc_start: 0.7897 (mmm) cc_final: 0.7546 (mpp) REVERT: 2 50 GLN cc_start: 0.7995 (tp40) cc_final: 0.7569 (mt0) REVERT: 2 57 GLU cc_start: 0.8743 (mp0) cc_final: 0.8487 (mp0) REVERT: 2 152 LYS cc_start: 0.8217 (pttt) cc_final: 0.7489 (mttm) REVERT: 2 179 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8928 (mt) REVERT: 2 421 ILE cc_start: 0.9147 (pt) cc_final: 0.8871 (pt) REVERT: 3 78 MET cc_start: 0.8243 (mmm) cc_final: 0.8000 (mmm) REVERT: 6 2 MET cc_start: 0.3463 (mmm) cc_final: 0.3015 (mmm) REVERT: 6 27 LYS cc_start: 0.7145 (mptt) cc_final: 0.6749 (mmmt) REVERT: 6 30 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: 6 90 ASN cc_start: 0.7429 (p0) cc_final: 0.6853 (p0) REVERT: g 30 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7330 (t80) REVERT: g 50 TYR cc_start: 0.7138 (m-10) cc_final: 0.6931 (m-10) REVERT: 9 46 GLU cc_start: 0.7999 (tp30) cc_final: 0.7738 (tp30) REVERT: C 523 ARG cc_start: 0.7251 (tpt-90) cc_final: 0.6813 (tpp-160) REVERT: C 531 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5076 (m-80) REVERT: C 633 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: A 70 LYS cc_start: 0.8106 (tptt) cc_final: 0.7681 (ptmt) REVERT: A 84 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8513 (mtm180) REVERT: A 92 MET cc_start: 0.7188 (tpp) cc_final: 0.6985 (tpp) REVERT: A 153 ASP cc_start: 0.8551 (t0) cc_final: 0.7957 (t0) REVERT: A 166 MET cc_start: 0.8922 (mtt) cc_final: 0.8626 (mtt) outliers start: 49 outliers final: 35 residues processed: 311 average time/residue: 0.1326 time to fit residues: 65.1391 Evaluate side-chains 294 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 U residue 142 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 63 LEU 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 63 SER Chi-restraints excluded: chain 2 residue 83 TYR Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 3 residue 105 GLU 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 g residue 30 PHE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain C residue 531 TYR 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 790 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 107 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 136 LEU 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: 0.4980 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN 2 198 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 = 0.3850 r_free = 0.3850 target = 0.142752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106450 restraints weight = 29360.126| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.34 r_work: 0.3261 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 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 = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20387 Z= 0.127 Angle : 0.536 8.039 27629 Z= 0.273 Chirality : 0.039 0.197 3178 Planarity : 0.004 0.070 3396 Dihedral : 9.841 157.425 2979 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.73 % Rotamer: Outliers : 2.62 % Allowed : 17.14 % Favored : 80.23 % 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: 1.88 (0.18), residues: 2413 helix: 2.19 (0.13), residues: 1573 sheet: -0.76 (0.60), residues: 75 loop : -0.55 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG 9 34 TYR 0.025 0.001 TYR A 194 PHE 0.025 0.001 PHE 1 224 TRP 0.022 0.001 TRP 1 125 HIS 0.005 0.001 HIS 9 24 Details of bonding type rmsd covalent geometry : bond 0.00296 (20381) covalent geometry : angle 0.53525 (27617) SS BOND : bond 0.00960 ( 6) SS BOND : angle 1.47845 ( 12) hydrogen bonds : bond 0.03699 ( 1232) hydrogen bonds : angle 3.90479 ( 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 317 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8284 (ttp) REVERT: D 46 ASP cc_start: 0.8446 (m-30) cc_final: 0.7666 (m-30) REVERT: U 59 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: W 94 GLU cc_start: 0.8668 (tp30) cc_final: 0.8398 (tp30) REVERT: X 19 TYR cc_start: 0.8569 (m-80) cc_final: 0.8342 (m-80) REVERT: X 109 LYS cc_start: 0.8385 (tppt) cc_final: 0.7943 (mtmt) REVERT: X 112 GLU cc_start: 0.7294 (tm-30) cc_final: 0.7023 (mt-10) REVERT: X 115 MET cc_start: 0.8133 (mmt) cc_final: 0.7898 (mmt) REVERT: X 124 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7866 (mm-30) REVERT: 1 21 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5674 (t80) REVERT: 1 88 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.6426 (t60) REVERT: 1 273 PHE cc_start: 0.7294 (t80) cc_final: 0.6718 (m-10) REVERT: 1 288 PHE cc_start: 0.7465 (m-10) cc_final: 0.7058 (t80) REVERT: 1 290 MET cc_start: 0.8216 (mmm) cc_final: 0.7786 (mpp) REVERT: 2 50 GLN cc_start: 0.8242 (tp40) cc_final: 0.7698 (mt0) REVERT: 2 152 LYS cc_start: 0.8416 (pttt) cc_final: 0.7648 (mttm) REVERT: 2 179 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8984 (mt) REVERT: 2 258 LEU cc_start: 0.8242 (tp) cc_final: 0.8005 (tt) REVERT: 2 421 ILE cc_start: 0.9201 (pt) cc_final: 0.8916 (pt) REVERT: 3 78 MET cc_start: 0.8426 (mmm) cc_final: 0.8209 (mmm) REVERT: 6 2 MET cc_start: 0.3471 (mmm) cc_final: 0.3035 (mmm) REVERT: 6 27 LYS cc_start: 0.7471 (mptt) cc_final: 0.6984 (mmmt) REVERT: 6 30 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7623 (tmm) REVERT: 6 90 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6661 (p0) REVERT: g 30 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7546 (t80) REVERT: 9 42 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8506 (mm-30) REVERT: 9 46 GLU cc_start: 0.8230 (tp30) cc_final: 0.7983 (tp30) REVERT: C 523 ARG cc_start: 0.7252 (tpt-90) cc_final: 0.6796 (tpp80) REVERT: C 633 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8254 (mtm) REVERT: C 804 TRP cc_start: 0.7353 (t60) cc_final: 0.6959 (t60) REVERT: A 70 LYS cc_start: 0.8013 (tptt) cc_final: 0.7599 (ptmt) REVERT: A 84 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8670 (mtm180) REVERT: A 92 MET cc_start: 0.7334 (tpp) cc_final: 0.7094 (tpp) REVERT: A 153 ASP cc_start: 0.8765 (t0) cc_final: 0.8207 (t0) REVERT: A 166 MET cc_start: 0.8982 (mtt) cc_final: 0.8691 (mtt) REVERT: A 209 LYS cc_start: 0.7013 (mtmt) cc_final: 0.6744 (mmmt) outliers start: 56 outliers final: 35 residues processed: 301 average time/residue: 0.1367 time to fit residues: 64.1661 Evaluate side-chains 296 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 10 VAL 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 85 ASP Chi-restraints excluded: chain U residue 91 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 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 88 TRP 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 63 SER Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 3 residue 105 GLU 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 g residue 64 LEU 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 790 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 107 GLU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 136 LEU 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: 6.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 229 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN b 52 ASN C 616 GLN A 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106575 restraints weight = 29218.708| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.29 r_work: 0.3266 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20387 Z= 0.118 Angle : 0.547 14.563 27629 Z= 0.274 Chirality : 0.038 0.163 3178 Planarity : 0.004 0.056 3396 Dihedral : 9.639 158.486 2979 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.69 % Rotamer: Outliers : 2.58 % Allowed : 17.19 % Favored : 80.23 % 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: 1.91 (0.18), residues: 2413 helix: 2.25 (0.13), residues: 1569 sheet: -0.89 (0.60), residues: 71 loop : -0.59 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 9 34 TYR 0.025 0.001 TYR A 194 PHE 0.021 0.001 PHE C 585 TRP 0.022 0.001 TRP 1 125 HIS 0.003 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00268 (20381) covalent geometry : angle 0.54608 (27617) SS BOND : bond 0.00549 ( 6) SS BOND : angle 1.93714 ( 12) hydrogen bonds : bond 0.03603 ( 1232) hydrogen bonds : angle 3.89802 ( 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 321 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (ttp) REVERT: D 46 ASP cc_start: 0.8468 (m-30) cc_final: 0.7657 (m-30) REVERT: L 37 ASN cc_start: 0.8783 (t0) cc_final: 0.8392 (t0) REVERT: W 94 GLU cc_start: 0.8692 (tp30) cc_final: 0.8479 (tp30) REVERT: X 23 ASP cc_start: 0.8463 (m-30) cc_final: 0.8241 (m-30) REVERT: X 109 LYS cc_start: 0.8433 (tppt) cc_final: 0.7974 (mtmt) REVERT: X 115 MET cc_start: 0.8124 (mmt) cc_final: 0.7847 (mmt) REVERT: X 124 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7913 (mm-30) REVERT: 1 21 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5730 (t80) REVERT: 1 86 ILE cc_start: 0.8403 (tt) cc_final: 0.7899 (pt) REVERT: 1 88 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.6438 (t60) REVERT: 1 273 PHE cc_start: 0.7325 (t80) cc_final: 0.6756 (m-10) REVERT: 1 288 PHE cc_start: 0.7453 (m-10) cc_final: 0.7089 (t80) REVERT: 1 290 MET cc_start: 0.8219 (mmm) cc_final: 0.7807 (mpp) REVERT: 2 38 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8605 (mp) REVERT: 2 50 GLN cc_start: 0.8274 (tp40) cc_final: 0.7731 (mt0) REVERT: 2 179 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8973 (mt) REVERT: 2 258 LEU cc_start: 0.8105 (tp) cc_final: 0.7895 (tt) REVERT: 2 421 ILE cc_start: 0.9175 (pt) cc_final: 0.8895 (pt) REVERT: 3 78 MET cc_start: 0.8431 (mmm) cc_final: 0.7889 (mmm) REVERT: 6 2 MET cc_start: 0.3157 (mmm) cc_final: 0.2734 (mmm) REVERT: 6 27 LYS cc_start: 0.7559 (mptt) cc_final: 0.7035 (mmmt) REVERT: 6 30 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7604 (tmm) REVERT: 6 90 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.6715 (p0) REVERT: g 30 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7579 (t80) REVERT: g 50 TYR cc_start: 0.7447 (m-10) cc_final: 0.7118 (m-10) REVERT: 9 46 GLU cc_start: 0.8185 (tp30) cc_final: 0.7937 (tp30) REVERT: C 523 ARG cc_start: 0.7243 (tpt-90) cc_final: 0.6796 (tpp80) REVERT: C 633 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8220 (mtm) REVERT: C 804 TRP cc_start: 0.7380 (t60) cc_final: 0.6953 (t60) REVERT: C 842 MET cc_start: 0.8131 (mmm) cc_final: 0.7845 (mmm) REVERT: A 70 LYS cc_start: 0.8000 (tptt) cc_final: 0.7599 (ptmt) REVERT: A 84 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8680 (mtm180) REVERT: A 92 MET cc_start: 0.7540 (tpp) cc_final: 0.7283 (tpp) REVERT: A 153 ASP cc_start: 0.8765 (t0) cc_final: 0.8373 (t70) REVERT: A 159 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8248 (mptt) REVERT: A 166 MET cc_start: 0.9031 (mtt) cc_final: 0.8731 (mtt) REVERT: A 209 LYS cc_start: 0.7008 (mtmt) cc_final: 0.6745 (mmmt) outliers start: 55 outliers final: 33 residues processed: 307 average time/residue: 0.1358 time to fit residues: 65.5754 Evaluate side-chains 294 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 10 VAL Chi-restraints excluded: chain U residue 31 THR Chi-restraints excluded: chain U residue 56 CYS 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 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 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 88 TRP 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 63 SER Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 179 LEU Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 3 residue 105 GLU 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 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 48 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 766 ASP Chi-restraints excluded: chain C residue 790 LEU 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 136 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 165 ASN b 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.136830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101626 restraints weight = 29371.180| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.28 r_work: 0.3192 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20387 Z= 0.167 Angle : 0.604 13.684 27629 Z= 0.305 Chirality : 0.041 0.228 3178 Planarity : 0.004 0.057 3396 Dihedral : 9.681 158.965 2979 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 2.34 % Allowed : 17.89 % Favored : 79.77 % 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: 1.72 (0.17), residues: 2413 helix: 2.03 (0.13), residues: 1578 sheet: -0.78 (0.64), residues: 67 loop : -0.56 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG W 47 TYR 0.025 0.001 TYR A 194 PHE 0.038 0.002 PHE g 8 TRP 0.018 0.001 TRP 1 125 HIS 0.005 0.001 HIS C 654 Details of bonding type rmsd covalent geometry : bond 0.00402 (20381) covalent geometry : angle 0.60305 (27617) SS BOND : bond 0.00649 ( 6) SS BOND : angle 1.95684 ( 12) hydrogen bonds : bond 0.04216 ( 1232) hydrogen bonds : angle 4.02836 ( 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 305 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8227 (ttp) REVERT: D 46 ASP cc_start: 0.8539 (m-30) cc_final: 0.7715 (m-30) REVERT: L 19 ARG cc_start: 0.5842 (ttt90) cc_final: 0.5641 (ttm170) REVERT: U 70 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7634 (ttmm) REVERT: U 71 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: W 94 GLU cc_start: 0.8627 (tp30) cc_final: 0.8395 (tp30) REVERT: X 109 LYS cc_start: 0.8365 (tppt) cc_final: 0.7822 (mttt) REVERT: X 115 MET cc_start: 0.8220 (mmt) cc_final: 0.7945 (mmt) REVERT: 1 21 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.6066 (t80) REVERT: 1 88 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.6585 (t60) REVERT: 1 125 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.8569 (m100) REVERT: 1 273 PHE cc_start: 0.7421 (t80) cc_final: 0.6919 (m-10) REVERT: 1 288 PHE cc_start: 0.7453 (m-10) cc_final: 0.7037 (t80) REVERT: 1 290 MET cc_start: 0.8255 (mmm) cc_final: 0.7806 (mpp) REVERT: 1 307 ASN cc_start: 0.8304 (t0) cc_final: 0.7823 (t0) REVERT: 2 38 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8731 (mp) REVERT: 2 50 GLN cc_start: 0.8421 (tp40) cc_final: 0.7840 (mt0) REVERT: 3 78 MET cc_start: 0.8553 (mmm) cc_final: 0.8142 (mmm) REVERT: 6 2 MET cc_start: 0.3351 (mmm) cc_final: 0.2947 (mmm) REVERT: 6 27 LYS cc_start: 0.7791 (mptt) cc_final: 0.7296 (mmtt) REVERT: 6 30 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7718 (tmm) REVERT: 6 90 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6627 (p0) REVERT: g 30 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7428 (t80) REVERT: g 60 GLN cc_start: 0.8466 (mt0) cc_final: 0.8146 (tt0) REVERT: 9 46 GLU cc_start: 0.8279 (tp30) cc_final: 0.8022 (tp30) REVERT: C 523 ARG cc_start: 0.7199 (tpt-90) cc_final: 0.6744 (tpp80) REVERT: C 534 MET cc_start: 0.7621 (mmp) cc_final: 0.7389 (mmp) REVERT: C 633 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: C 804 TRP cc_start: 0.7296 (t60) cc_final: 0.6857 (t60) REVERT: C 842 MET cc_start: 0.8148 (mmm) cc_final: 0.7944 (mmm) REVERT: A 70 LYS cc_start: 0.8029 (tptt) cc_final: 0.7754 (tptp) REVERT: A 84 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8732 (mtm180) REVERT: A 92 MET cc_start: 0.7233 (tpp) cc_final: 0.6998 (tpp) REVERT: A 153 ASP cc_start: 0.8857 (t0) cc_final: 0.8320 (t0) REVERT: A 159 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8302 (mptt) REVERT: A 166 MET cc_start: 0.9074 (mtt) cc_final: 0.8831 (mtt) REVERT: A 209 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6743 (mmmt) outliers start: 50 outliers final: 27 residues processed: 290 average time/residue: 0.1474 time to fit residues: 66.3673 Evaluate side-chains 289 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 56 CYS Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 91 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 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 88 TRP Chi-restraints excluded: chain 1 residue 125 TRP 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 63 SER Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 163 ILE Chi-restraints excluded: chain 2 residue 466 VAL Chi-restraints excluded: chain 3 residue 105 GLU 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 16 LEU Chi-restraints excluded: chain g residue 30 PHE 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 790 LEU 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 159 LYS 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: 0.9980 chunk 122 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 165 ASN b 52 ASN C 537 GLN C 694 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104503 restraints weight = 29241.578| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.25 r_work: 0.3239 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20387 Z= 0.114 Angle : 0.557 13.782 27629 Z= 0.279 Chirality : 0.039 0.210 3178 Planarity : 0.004 0.058 3396 Dihedral : 9.414 160.387 2979 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 1.83 % Allowed : 18.59 % Favored : 79.58 % 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: 1.88 (0.18), residues: 2413 helix: 2.19 (0.13), residues: 1576 sheet: -0.84 (0.61), residues: 71 loop : -0.56 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 34 TYR 0.024 0.001 TYR A 194 PHE 0.028 0.001 PHE g 8 TRP 0.017 0.001 TRP 1 125 HIS 0.003 0.001 HIS X 164 Details of bonding type rmsd covalent geometry : bond 0.00256 (20381) covalent geometry : angle 0.55639 (27617) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.54640 ( 12) hydrogen bonds : bond 0.03661 ( 1232) hydrogen bonds : angle 3.89938 ( 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 304 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: D 25 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8353 (mtp) REVERT: D 46 ASP cc_start: 0.8554 (m-30) cc_final: 0.7619 (m-30) REVERT: W 94 GLU cc_start: 0.8626 (tp30) cc_final: 0.8396 (tp30) REVERT: W 97 LYS cc_start: 0.8498 (tppt) cc_final: 0.8092 (mmtp) REVERT: X 109 LYS cc_start: 0.8406 (tppt) cc_final: 0.7876 (mttt) REVERT: X 115 MET cc_start: 0.8175 (mmt) cc_final: 0.7900 (mmt) REVERT: 1 21 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5996 (t80) REVERT: 1 88 TRP cc_start: 0.8557 (OUTLIER) cc_final: 0.6437 (t60) REVERT: 1 125 TRP cc_start: 0.8736 (OUTLIER) cc_final: 0.8535 (m100) REVERT: 1 273 PHE cc_start: 0.7413 (t80) cc_final: 0.6961 (m-10) REVERT: 1 288 PHE cc_start: 0.7412 (m-10) cc_final: 0.7109 (t80) REVERT: 1 290 MET cc_start: 0.8071 (mmm) cc_final: 0.7716 (mpp) REVERT: 1 307 ASN cc_start: 0.8175 (t0) cc_final: 0.7707 (t0) REVERT: 2 50 GLN cc_start: 0.8376 (tp40) cc_final: 0.7756 (mt0) REVERT: 3 78 MET cc_start: 0.8425 (mmm) cc_final: 0.7974 (mmm) REVERT: 6 2 MET cc_start: 0.3565 (mmm) cc_final: 0.3153 (mmm) REVERT: 6 27 LYS cc_start: 0.7778 (mptt) cc_final: 0.7284 (mmtt) REVERT: 6 30 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7589 (tmm) REVERT: 6 90 ASN cc_start: 0.7065 (p0) cc_final: 0.6478 (p0) REVERT: g 30 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7584 (t80) REVERT: g 50 TYR cc_start: 0.7541 (m-10) cc_final: 0.7229 (m-10) REVERT: g 60 GLN cc_start: 0.8464 (mt0) cc_final: 0.8155 (tt0) REVERT: b 62 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6371 (tt0) REVERT: 9 46 GLU cc_start: 0.8237 (tp30) cc_final: 0.7967 (tp30) REVERT: C 523 ARG cc_start: 0.7204 (tpt-90) cc_final: 0.6750 (tpp80) REVERT: C 531 TYR cc_start: 0.6181 (t80) cc_final: 0.5344 (m-80) REVERT: C 633 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8168 (mtm) REVERT: C 804 TRP cc_start: 0.7388 (t60) cc_final: 0.6939 (t60) REVERT: C 842 MET cc_start: 0.8061 (mmm) cc_final: 0.7861 (mmm) REVERT: A 70 LYS cc_start: 0.7960 (tptt) cc_final: 0.7741 (ptmt) REVERT: A 84 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8720 (mtm180) REVERT: A 92 MET cc_start: 0.7203 (tpp) cc_final: 0.6958 (tpp) REVERT: A 153 ASP cc_start: 0.8786 (t0) cc_final: 0.8438 (t70) REVERT: A 159 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8147 (mptt) REVERT: A 209 LYS cc_start: 0.6965 (mtmt) cc_final: 0.6757 (mmmt) outliers start: 39 outliers final: 23 residues processed: 290 average time/residue: 0.1441 time to fit residues: 64.9317 Evaluate side-chains 287 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 56 CYS Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 142 VAL Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain 1 residue 21 TYR Chi-restraints excluded: chain 1 residue 88 TRP Chi-restraints excluded: chain 1 residue 125 TRP 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 63 SER 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 87 VAL Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 30 PHE Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 665 VAL 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 159 LYS 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: 7.9990 chunk 206 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 52 ASN ** C 537 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 = 0.3815 r_free = 0.3815 target = 0.139491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104098 restraints weight = 29165.430| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.29 r_work: 0.3224 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20387 Z= 0.126 Angle : 0.566 13.361 27629 Z= 0.284 Chirality : 0.039 0.216 3178 Planarity : 0.004 0.058 3396 Dihedral : 9.309 160.531 2979 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 1.64 % Allowed : 18.50 % Favored : 79.86 % 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: 1.93 (0.18), residues: 2413 helix: 2.24 (0.13), residues: 1570 sheet: -0.97 (0.64), residues: 63 loop : -0.52 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG 9 34 TYR 0.025 0.001 TYR A 194 PHE 0.028 0.001 PHE g 8 TRP 0.016 0.001 TRP 1 125 HIS 0.003 0.001 HIS C 800 Details of bonding type rmsd covalent geometry : bond 0.00293 (20381) covalent geometry : angle 0.56550 (27617) SS BOND : bond 0.00496 ( 6) SS BOND : angle 1.64968 ( 12) hydrogen bonds : bond 0.03718 ( 1232) hydrogen bonds : angle 3.89805 ( 3591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5473.78 seconds wall clock time: 94 minutes 9.79 seconds (5649.79 seconds total)