Starting phenix.real_space_refine on Tue Sep 15 20:33:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6k_21558/09_2026/6w6k_21558.map" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 1534 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 23419 2.51 5 N 8753 2.21 5 O 13183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46934 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 32917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32917 Classifications: {'RNAv2': 1534} Modifications used: {'rna2p_pur': 108, 'rna2p_pyr': 77, 'rna3p_pur': 767, 'rna3p_pyr': 582} Link IDs: {'rna2p': 185, 'rna3p': 1348} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 622 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 7, 'TYR:plan': 5, 'ARG:plan': 19, 'PHE:plan': 4, 'GLU:plan': 8, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 240 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 559 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ARG:plan': 15, 'ASN:plan1': 2, 'ASP:plan': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "P" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 629 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "T" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 659 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.57, per 1000 atoms: 0.18 Number of scatterers: 46934 At special positions: 0 Unit cell: (202.797, 218.892, 164.169, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 1534 15.00 Mg 1 11.99 O 13183 8.00 N 8753 7.00 C 23419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 34.2% alpha, 11.0% beta 434 base pairs and 779 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.673A pdb=" N LEU C 11 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 removed outlier: 4.108A pdb=" N LEU C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.003A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 77' Processing helix chain 'C' and resid 84 through 93 removed outlier: 4.014A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.573A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.901A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 14 removed outlier: 3.895A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 48 through 63 removed outlier: 3.630A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.611A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.562A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 157 through 164 removed outlier: 3.806A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.544A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 67 removed outlier: 3.617A pdb=" N ALA E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 117 removed outlier: 3.967A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 145 removed outlier: 3.501A pdb=" N ASN E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'H' and resid 5 through 15 removed outlier: 3.616A pdb=" N LEU H 10 " --> pdb=" O ILE H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 removed outlier: 3.521A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.807A pdb=" N LEU H 91 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 48 removed outlier: 4.025A pdb=" N VAL I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.808A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP I 90 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 3.942A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.701A pdb=" N LEU J 17 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 27 removed outlier: 3.512A pdb=" N VAL J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 22 through 27' Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.679A pdb=" N VAL K 64 " --> pdb=" O PHE K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 removed outlier: 3.638A pdb=" N ASP K 71 " --> pdb=" O ARG K 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 93 through 103 removed outlier: 3.827A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.922A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL L 7 " --> pdb=" O VAL L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 7' Processing helix chain 'M' and resid 13 through 20 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 48 through 58 removed outlier: 4.232A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 80 removed outlier: 3.575A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 2 through 19 removed outlier: 3.807A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 27 Processing helix chain 'N' and resid 41 through 47 removed outlier: 4.133A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.679A pdb=" N VAL N 83 " --> pdb=" O SER N 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.869A pdb=" N ALA O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 4.044A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.840A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.789A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.853A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 60 removed outlier: 4.134A pdb=" N ARG R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'S' and resid 11 through 22 removed outlier: 3.642A pdb=" N LEU S 15 " --> pdb=" O ASP S 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 69 through 73 removed outlier: 3.530A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 69 through 73' Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.575A pdb=" N GLN T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 63 Proline residue: T 55 - end of helix removed outlier: 3.579A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.696A pdb=" N HIS T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 5.933A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA5, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 17 removed outlier: 7.423A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL E 17 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR E 33 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 87 Processing sheet with id=AA8, first strand: chain 'F' and resid 63 through 64 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 27 removed outlier: 3.708A pdb=" N MET H 26 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'H' and resid 75 through 76 removed outlier: 3.798A pdb=" N GLU H 123 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.314A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 44 through 45 removed outlier: 3.997A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER J 101 " --> pdb=" O ARG J 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 48 through 49 removed outlier: 4.032A pdb=" N GLU J 66 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 40 through 43 removed outlier: 7.099A pdb=" N ILE K 33 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP K 43 " --> pdb=" O VAL K 31 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL K 31 " --> pdb=" O TRP K 43 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA K 20 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS K 86 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE K 22 " --> pdb=" O LYS K 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 51 through 55 Processing sheet with id=AB8, first strand: chain 'Q' and resid 7 through 9 removed outlier: 3.962A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG Q 61 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU Q 74 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS Q 63 " --> pdb=" O TRP Q 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP Q 72 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS Q 70 " --> pdb=" O PRO Q 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AC1, first strand: chain 'Q' and resid 25 through 29 removed outlier: 4.309A pdb=" N VAL Q 28 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE Q 37 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 47 through 51 removed outlier: 3.826A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1097 hydrogen bonds 1778 hydrogen bond angles 0 basepair planarities 434 basepair parallelities 779 stacking parallelities Total time for adding SS restraints: 18.16 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8065 1.33 - 1.45: 20716 1.45 - 1.57: 19135 1.57 - 1.69: 3067 1.69 - 1.81: 77 Bond restraints: 51060 Sorted by residual: bond pdb=" N LEU J 92 " pdb=" CA LEU J 92 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.30e-02 5.92e+03 6.33e+00 bond pdb=" N LYS F 53 " pdb=" CA LYS F 53 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.23e+00 bond pdb=" N ASP J 91 " pdb=" CA ASP J 91 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.44e-02 4.82e+03 4.76e+00 bond pdb=" C THR L 39 " pdb=" N THR L 40 " ideal model delta sigma weight residual 1.331 1.377 -0.046 2.83e-02 1.25e+03 2.60e+00 bond pdb=" C3' U A1528 " pdb=" O3' U A1528 " ideal model delta sigma weight residual 1.415 1.446 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 51055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 72338 2.13 - 4.26: 3929 4.26 - 6.40: 348 6.40 - 8.53: 8 8.53 - 10.66: 2 Bond angle restraints: 76625 Sorted by residual: angle pdb=" C3' U A1528 " pdb=" O3' U A1528 " pdb=" P G A1529 " ideal model delta sigma weight residual 119.70 125.77 -6.07 1.20e+00 6.94e-01 2.56e+01 angle pdb=" C3' A A1101 " pdb=" O3' A A1101 " pdb=" P A A1102 " ideal model delta sigma weight residual 119.70 125.60 -5.90 1.20e+00 6.94e-01 2.42e+01 angle pdb=" C3' U A1065 " pdb=" O3' U A1065 " pdb=" P C A1066 " ideal model delta sigma weight residual 119.70 125.55 -5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" C3' A A1201 " pdb=" O3' A A1201 " pdb=" P U A1202 " ideal model delta sigma weight residual 119.70 125.52 -5.82 1.20e+00 6.94e-01 2.35e+01 angle pdb=" C3' G A 484 " pdb=" O3' G A 484 " pdb=" P U A 485 " ideal model delta sigma weight residual 119.70 125.26 -5.56 1.20e+00 6.94e-01 2.14e+01 ... (remaining 76620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 24374 34.99 - 69.98: 2564 69.98 - 104.96: 210 104.96 - 139.95: 2 139.95 - 174.94: 6 Dihedral angle restraints: 27156 sinusoidal: 21804 harmonic: 5352 Sorted by residual: dihedral pdb=" C4' A A 451 " pdb=" C3' A A 451 " pdb=" C2' A A 451 " pdb=" C1' A A 451 " ideal model delta sinusoidal sigma weight residual 36.35 -38.34 74.68 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' G A 575 " pdb=" C3' G A 575 " pdb=" C2' G A 575 " pdb=" C1' G A 575 " ideal model delta sinusoidal sigma weight residual 36.35 -37.84 74.19 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' A A 71 " pdb=" C3' A A 71 " pdb=" C2' A A 71 " pdb=" C1' A A 71 " ideal model delta sinusoidal sigma weight residual 36.34 -37.76 74.11 1 3.10e+00 1.04e-01 7.25e+02 ... (remaining 27153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7673 0.075 - 0.151: 264 0.151 - 0.226: 345 0.226 - 0.302: 1562 0.302 - 0.377: 11 Chirality restraints: 9855 Sorted by residual: chirality pdb=" P A A 373 " pdb=" OP1 A A 373 " pdb=" OP2 A A 373 " pdb=" O5' A A 373 " both_signs ideal model delta sigma weight residual True 2.17 -2.55 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" P U A1202 " pdb=" OP1 U A1202 " pdb=" OP2 U A1202 " pdb=" O5' U A1202 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" P A A 329 " pdb=" OP1 A A 329 " pdb=" OP2 A A 329 " pdb=" O5' A A 329 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 9852 not shown) Planarity restraints: 4028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 748 " 0.027 2.00e-02 2.50e+03 1.28e-02 4.93e+00 pdb=" N9 G A 748 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G A 748 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 748 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 748 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 748 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G A 748 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G A 748 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G A 748 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 748 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 748 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 748 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1319 " 0.023 2.00e-02 2.50e+03 1.19e-02 3.87e+00 pdb=" N9 A A1319 " -0.030 2.00e-02 2.50e+03 pdb=" C8 A A1319 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A A1319 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A A1319 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A1319 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A A1319 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A A1319 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1319 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1319 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A A1319 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 745 " 0.021 2.00e-02 2.50e+03 1.11e-02 3.70e+00 pdb=" N9 G A 745 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G A 745 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 745 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 745 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 745 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A 745 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G A 745 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 745 " 0.013 2.00e-02 2.50e+03 pdb=" N2 G A 745 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G A 745 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 745 " 0.001 2.00e-02 2.50e+03 ... (remaining 4025 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 2432 2.67 - 3.23: 39972 3.23 - 3.79: 89640 3.79 - 4.34: 115137 4.34 - 4.90: 154809 Nonbonded interactions: 401990 Sorted by model distance: nonbonded pdb=" OP1 G A 126 " pdb=" O2' U A 605 " model vdw 2.113 3.040 nonbonded pdb=" N6 A A 71 " pdb=" O2 C A 99 " model vdw 2.146 3.120 nonbonded pdb=" OG1 THR E 79 " pdb=" O ASN E 121 " model vdw 2.159 3.040 nonbonded pdb=" OP1 U A 123 " pdb=" O2' C A 311 " model vdw 2.159 3.040 nonbonded pdb=" O2' A A 767 " pdb=" O2' C A1524 " model vdw 2.175 3.040 ... (remaining 401985 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 52.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 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 : 0.003 0.046 51060 Z= 0.134 Angle : 0.851 10.661 76625 Z= 0.357 Chirality : 0.109 0.377 9855 Planarity : 0.003 0.028 4028 Dihedral : 20.390 174.938 23694 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -4.28 (0.16), residues: 1833 helix: -2.44 (0.18), residues: 532 sheet: -2.16 (0.31), residues: 245 loop : -3.36 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 62 TYR 0.017 0.001 TYR D 3 PHE 0.011 0.001 PHE S 9 TRP 0.004 0.001 TRP C 166 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (51060) covalent geometry : angle 0.85113 / 0.36 (76625) hydrogen bonds : bond 0.11605 / 5.91 ( 1509) hydrogen bonds : angle 4.91005 / 1.99 ( 2948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 82 ASP cc_start: 0.4107 (m-30) cc_final: 0.3869 (m-30) REVERT: D 88 ASN cc_start: 0.5746 (t0) cc_final: 0.5505 (t0) REVERT: E 151 MET cc_start: 0.4923 (mmm) cc_final: 0.4566 (ttm) REVERT: J 80 THR cc_start: 0.3416 (p) cc_final: 0.3075 (p) REVERT: N 60 ARG cc_start: 0.4010 (pmt170) cc_final: 0.3541 (tpp-160) REVERT: P 52 LEU cc_start: 0.6489 (mp) cc_final: 0.6281 (mp) REVERT: S 33 TRP cc_start: 0.4548 (m-90) cc_final: 0.4276 (m100) REVERT: S 75 PRO cc_start: 0.7651 (Cg_endo) cc_final: 0.7406 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.3655 time to fit residues: 257.9250 Evaluate side-chains 300 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 HIS C 18 ASN C 24 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 151 GLN D 197 HIS E 18 ASN E 77 ASN E 134 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN H 117 GLN K 14 GLN K 23 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN N 42 ASN N 61 ASN O 41 HIS ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.169006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.159533 restraints weight = 167949.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.161755 restraints weight = 71998.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.163054 restraints weight = 37935.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.163850 restraints weight = 23613.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.164290 restraints weight = 16917.729| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 51060 Z= 0.319 Angle : 1.493 25.043 76625 Z= 0.586 Chirality : 0.111 1.525 9855 Planarity : 0.006 0.062 4028 Dihedral : 18.941 177.748 20462 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 4.22 % Allowed : 16.86 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.88 (0.17), residues: 1833 helix: -1.76 (0.20), residues: 548 sheet: -2.36 (0.26), residues: 312 loop : -3.23 (0.17), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 58 TYR 0.018 0.002 TYR E 49 PHE 0.033 0.003 PHE Q 27 TRP 0.025 0.004 TRP C 17 HIS 0.008 0.002 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.32 (51060) covalent geometry : angle 1.49343 / 0.59 (76625) hydrogen bonds : bond 0.09972 / 5.23 ( 1509) hydrogen bonds : angle 3.88391 / 1.55 ( 2948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 ASN cc_start: 0.6902 (t0) cc_final: 0.6690 (t0) REVERT: D 94 GLU cc_start: 0.7256 (tp30) cc_final: 0.6966 (tp30) REVERT: F 5 GLU cc_start: 0.6750 (mp0) cc_final: 0.6532 (mp0) REVERT: F 9 MET cc_start: 0.7728 (ptp) cc_final: 0.7309 (pmm) REVERT: H 37 ASN cc_start: 0.7697 (m-40) cc_final: 0.7424 (m110) REVERT: L 72 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7617 (p0) REVERT: N 8 ARG cc_start: 0.5784 (mmt180) cc_final: 0.5296 (mmt90) REVERT: N 60 ARG cc_start: 0.5320 (pmt170) cc_final: 0.3924 (tpp-160) REVERT: O 58 MET cc_start: 0.6704 (mmm) cc_final: 0.6488 (mmm) REVERT: P 31 ARG cc_start: 0.8515 (tpt-90) cc_final: 0.8284 (ttt180) REVERT: P 70 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7496 (tpp80) outliers start: 57 outliers final: 38 residues processed: 353 average time/residue: 0.3198 time to fit residues: 176.6532 Evaluate side-chains 318 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 127 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 328 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 chunk 213 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS E 77 ASN E 121 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS N 59 GLN O 41 HIS O 61 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.169601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.160344 restraints weight = 167832.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.162580 restraints weight = 70831.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.163887 restraints weight = 36759.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.164657 restraints weight = 22593.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.165170 restraints weight = 16142.436| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 51060 Z= 0.207 Angle : 1.163 21.610 76625 Z= 0.463 Chirality : 0.090 1.242 9855 Planarity : 0.005 0.074 4028 Dihedral : 19.060 179.529 20462 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.10 % Allowed : 20.19 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.30 (0.18), residues: 1833 helix: -1.05 (0.21), residues: 551 sheet: -2.13 (0.27), residues: 317 loop : -2.99 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 51 TYR 0.012 0.002 TYR C 167 PHE 0.015 0.002 PHE C 129 TRP 0.017 0.002 TRP N 41 HIS 0.022 0.002 HIS K 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 (51060) covalent geometry : angle 1.16338 / 0.46 (76625) hydrogen bonds : bond 0.08340 / 4.43 ( 1509) hydrogen bonds : angle 3.57960 / 1.42 ( 2948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 314 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 ASN cc_start: 0.6762 (t0) cc_final: 0.6550 (t0) REVERT: D 123 MET cc_start: 0.6580 (ttt) cc_final: 0.6164 (ttm) REVERT: F 52 ASN cc_start: 0.5804 (t0) cc_final: 0.5584 (t0) REVERT: J 81 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7297 (tp30) REVERT: L 82 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7999 (ttm-80) REVERT: N 8 ARG cc_start: 0.5381 (mmt180) cc_final: 0.4946 (mmt90) REVERT: N 60 ARG cc_start: 0.5241 (pmt170) cc_final: 0.4508 (tpm170) REVERT: P 70 ARG cc_start: 0.7755 (tpt-90) cc_final: 0.7240 (tpp80) REVERT: Q 35 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5838 (tmtt) REVERT: R 51 GLN cc_start: 0.5065 (OUTLIER) cc_final: 0.4653 (pm20) REVERT: S 12 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5620 (pp) REVERT: S 14 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6386 (pp) outliers start: 69 outliers final: 35 residues processed: 356 average time/residue: 0.3253 time to fit residues: 182.2770 Evaluate side-chains 320 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 128 optimal weight: 9.9990 chunk 229 optimal weight: 0.0050 chunk 102 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 overall best weight: 6.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 73 ASN D 99 ASN D 119 HIS E 77 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN J 20 GLN J 56 HIS ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN L 28 GLN N 42 ASN ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS T 54 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.157091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148077 restraints weight = 168409.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.150220 restraints weight = 70516.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.151493 restraints weight = 36527.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152252 restraints weight = 22349.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.152705 restraints weight = 15866.809| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 51060 Z= 0.420 Angle : 1.630 27.949 76625 Z= 0.646 Chirality : 0.114 1.384 9855 Planarity : 0.008 0.127 4028 Dihedral : 19.791 178.433 20462 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.62 % Favored : 85.27 % Rotamer: Outliers : 7.69 % Allowed : 21.97 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.17), residues: 1833 helix: -1.77 (0.19), residues: 565 sheet: -2.41 (0.28), residues: 300 loop : -3.34 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 64 TYR 0.032 0.004 TYR C 192 PHE 0.028 0.004 PHE C 202 TRP 0.036 0.004 TRP Q 72 HIS 0.015 0.003 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.42 (51060) covalent geometry : angle 1.63037 / 0.65 (76625) hydrogen bonds : bond 0.13179 / 6.95 ( 1509) hydrogen bonds : angle 4.52507 / 1.78 ( 2948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 297 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 LEU cc_start: 0.4806 (OUTLIER) cc_final: 0.4442 (tt) REVERT: C 48 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6367 (pptt) REVERT: C 109 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6625 (mm-30) REVERT: C 192 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6149 (p90) REVERT: D 103 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7234 (ptm160) REVERT: D 123 MET cc_start: 0.6960 (ttt) cc_final: 0.6537 (ttm) REVERT: J 97 ASP cc_start: 0.3902 (p0) cc_final: 0.3613 (p0) REVERT: K 36 ARG cc_start: 0.6614 (mtt180) cc_final: 0.6286 (mtt180) REVERT: K 84 MET cc_start: 0.6000 (ttm) cc_final: 0.5393 (ptm) REVERT: L 24 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5785 (mp0) REVERT: L 82 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8078 (ttm-80) REVERT: N 58 ARG cc_start: 0.6607 (mtt90) cc_final: 0.6259 (mtm-85) REVERT: N 60 ARG cc_start: 0.5032 (pmt170) cc_final: 0.4614 (tpm170) REVERT: O 58 MET cc_start: 0.7128 (mmm) cc_final: 0.6876 (mmp) REVERT: P 70 ARG cc_start: 0.7922 (tpt-90) cc_final: 0.7493 (tpp80) REVERT: S 12 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.5968 (pp) REVERT: S 14 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6073 (pp) REVERT: S 64 GLU cc_start: 0.2337 (OUTLIER) cc_final: 0.1768 (tt0) outliers start: 104 outliers final: 65 residues processed: 368 average time/residue: 0.3258 time to fit residues: 188.4463 Evaluate side-chains 340 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 54 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 169 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 184 optimal weight: 0.4980 chunk 139 optimal weight: 8.9990 chunk 303 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 119 HIS E 77 ASN E 121 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN J 56 HIS K 23 HIS K 28 ASN N 48 GLN O 50 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.162724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.153564 restraints weight = 164057.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155801 restraints weight = 68528.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.157106 restraints weight = 35284.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.157930 restraints weight = 21568.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.158422 restraints weight = 15125.858| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 51060 Z= 0.220 Angle : 1.239 16.587 76625 Z= 0.493 Chirality : 0.093 1.280 9855 Planarity : 0.005 0.071 4028 Dihedral : 19.447 179.694 20462 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.47 % Allowed : 26.26 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.18), residues: 1833 helix: -1.28 (0.20), residues: 561 sheet: -2.21 (0.27), residues: 304 loop : -3.15 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 72 TYR 0.024 0.002 TYR L 94 PHE 0.028 0.002 PHE N 72 TRP 0.019 0.002 TRP D 169 HIS 0.010 0.002 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (51060) covalent geometry : angle 1.23898 / 0.49 (76625) hydrogen bonds : bond 0.09334 / 4.94 ( 1509) hydrogen bonds : angle 3.90073 / 1.56 ( 2948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 58 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8606 (mm-40) REVERT: D 94 GLU cc_start: 0.6969 (tp30) cc_final: 0.6513 (tp30) REVERT: D 170 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7347 (pp) REVERT: E 19 ARG cc_start: 0.8148 (tpt170) cc_final: 0.7660 (tpt170) REVERT: F 4 TYR cc_start: -0.1781 (OUTLIER) cc_final: -0.3940 (m-80) REVERT: F 9 MET cc_start: 0.7966 (pmm) cc_final: 0.7664 (pmm) REVERT: F 75 GLU cc_start: 0.0580 (OUTLIER) cc_final: 0.0041 (tt0) REVERT: K 84 MET cc_start: 0.5705 (ttm) cc_final: 0.5174 (ptm) REVERT: L 24 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: L 66 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6411 (mt) REVERT: L 82 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8087 (ttm-80) REVERT: N 58 ARG cc_start: 0.6528 (mtt90) cc_final: 0.6189 (mtm-85) REVERT: N 60 ARG cc_start: 0.4252 (pmt170) cc_final: 0.3678 (tpm170) REVERT: P 34 GLU cc_start: 0.8085 (pm20) cc_final: 0.7760 (pm20) REVERT: P 70 ARG cc_start: 0.7733 (tpt-90) cc_final: 0.7138 (tpp80) REVERT: S 12 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5865 (pp) REVERT: S 14 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6482 (pp) outliers start: 74 outliers final: 47 residues processed: 340 average time/residue: 0.3175 time to fit residues: 170.8956 Evaluate side-chains 324 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 130 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 317 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 HIS ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN H 15 ASN K 23 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.158174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149307 restraints weight = 167174.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.151441 restraints weight = 69836.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.152707 restraints weight = 36167.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.153487 restraints weight = 22134.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153972 restraints weight = 15566.277| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 51060 Z= 0.304 Angle : 1.416 20.610 76625 Z= 0.561 Chirality : 0.102 1.380 9855 Planarity : 0.007 0.102 4028 Dihedral : 19.683 179.844 20462 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.49 % Favored : 84.45 % Rotamer: Outliers : 7.10 % Allowed : 26.11 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.18), residues: 1833 helix: -1.36 (0.20), residues: 555 sheet: -2.44 (0.28), residues: 277 loop : -3.12 (0.17), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 76 TYR 0.028 0.002 TYR C 167 PHE 0.026 0.003 PHE C 202 TRP 0.042 0.004 TRP Q 72 HIS 0.017 0.003 HIS K 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.30 (51060) covalent geometry : angle 1.41586 / 0.56 (76625) hydrogen bonds : bond 0.11328 / 5.90 ( 1509) hydrogen bonds : angle 4.28323 / 1.71 ( 2948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 296 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6679 (pptt) REVERT: D 58 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8494 (mm-40) REVERT: D 94 GLU cc_start: 0.7293 (tp30) cc_final: 0.6527 (tp30) REVERT: D 103 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7223 (ptm160) REVERT: D 135 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7007 (tm-30) REVERT: D 170 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7349 (pp) REVERT: F 4 TYR cc_start: -0.1245 (OUTLIER) cc_final: -0.2628 (m-80) REVERT: H 76 ARG cc_start: 0.5826 (OUTLIER) cc_final: 0.4664 (tpp80) REVERT: N 22 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6915 (ptpp) REVERT: N 58 ARG cc_start: 0.6605 (mtt90) cc_final: 0.6282 (tpp80) REVERT: N 60 ARG cc_start: 0.4717 (pmt170) cc_final: 0.3800 (tpm170) REVERT: N 80 ARG cc_start: 0.7620 (tmm-80) cc_final: 0.7245 (tmm-80) REVERT: O 58 MET cc_start: 0.7518 (mmt) cc_final: 0.7220 (mmp) REVERT: P 70 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7202 (tpp80) REVERT: Q 80 LYS cc_start: 0.7311 (pptt) cc_final: 0.7006 (pptt) REVERT: R 62 ARG cc_start: 0.3995 (tpp80) cc_final: 0.2735 (mtt180) REVERT: S 12 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6024 (pp) REVERT: S 14 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6154 (pp) REVERT: S 64 GLU cc_start: 0.2599 (OUTLIER) cc_final: 0.1990 (tt0) REVERT: T 51 ASN cc_start: 0.7773 (m-40) cc_final: 0.7452 (m110) outliers start: 96 outliers final: 64 residues processed: 357 average time/residue: 0.3180 time to fit residues: 179.3285 Evaluate side-chains 352 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain T residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 198 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 300 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS E 77 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.153604 restraints weight = 165149.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.155832 restraints weight = 68373.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.157155 restraints weight = 35025.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.157950 restraints weight = 21196.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.158475 restraints weight = 14817.098| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 51060 Z= 0.209 Angle : 1.205 16.157 76625 Z= 0.479 Chirality : 0.090 1.328 9855 Planarity : 0.005 0.071 4028 Dihedral : 19.395 179.493 20462 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 6.36 % Allowed : 28.33 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.18), residues: 1833 helix: -1.01 (0.21), residues: 548 sheet: -2.32 (0.28), residues: 289 loop : -2.95 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 10 TYR 0.035 0.002 TYR L 94 PHE 0.041 0.002 PHE N 72 TRP 0.036 0.003 TRP Q 72 HIS 0.008 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (51060) covalent geometry : angle 1.20470 / 0.48 (76625) hydrogen bonds : bond 0.09143 / 4.81 ( 1509) hydrogen bonds : angle 3.88840 / 1.56 ( 2948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 305 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6419 (pptt) REVERT: C 52 SER cc_start: 0.7932 (OUTLIER) cc_final: 0.7364 (p) REVERT: D 94 GLU cc_start: 0.7026 (tp30) cc_final: 0.6615 (tp30) REVERT: D 120 LYS cc_start: 0.7694 (ttpt) cc_final: 0.7461 (pttm) REVERT: D 135 GLN cc_start: 0.7491 (tm-30) cc_final: 0.6933 (tm-30) REVERT: D 170 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7371 (pp) REVERT: E 70 MET cc_start: 0.6370 (tpp) cc_final: 0.6066 (tpp) REVERT: F 4 TYR cc_start: -0.1567 (OUTLIER) cc_final: -0.3216 (m-80) REVERT: F 9 MET cc_start: 0.8064 (pmm) cc_final: 0.7780 (pmm) REVERT: F 90 MET cc_start: 0.3106 (mmt) cc_final: 0.2581 (mmt) REVERT: H 9 MET cc_start: 0.4652 (tpp) cc_final: 0.4293 (tpp) REVERT: J 56 HIS cc_start: 0.6136 (OUTLIER) cc_final: 0.4432 (t-90) REVERT: J 62 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6059 (mtm110) REVERT: J 97 ASP cc_start: 0.2731 (p0) cc_final: 0.2444 (p0) REVERT: L 66 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6295 (mt) REVERT: L 82 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8320 (ttp80) REVERT: N 60 ARG cc_start: 0.4740 (pmt170) cc_final: 0.4088 (tpp-160) REVERT: P 34 GLU cc_start: 0.8090 (pm20) cc_final: 0.7840 (pm20) REVERT: P 42 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6559 (mm) REVERT: R 62 ARG cc_start: 0.3709 (tpp80) cc_final: 0.2602 (mtt180) REVERT: S 43 MET cc_start: 0.6628 (mmm) cc_final: 0.6277 (mmm) REVERT: S 64 GLU cc_start: 0.2367 (OUTLIER) cc_final: 0.1904 (tt0) REVERT: T 53 MET cc_start: 0.7726 (ttp) cc_final: 0.7480 (mtm) outliers start: 86 outliers final: 57 residues processed: 361 average time/residue: 0.3188 time to fit residues: 181.9901 Evaluate side-chains 349 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 64 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 5 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 218 optimal weight: 0.0570 chunk 40 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN S 42 ASN T 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.155992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.147383 restraints weight = 168498.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.149468 restraints weight = 70607.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.150687 restraints weight = 36535.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.151426 restraints weight = 22512.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.151919 restraints weight = 15975.049| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 51060 Z= 0.353 Angle : 1.509 20.394 76625 Z= 0.598 Chirality : 0.107 1.445 9855 Planarity : 0.007 0.091 4028 Dihedral : 19.881 178.611 20462 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.80 % Favored : 83.20 % Rotamer: Outliers : 7.54 % Allowed : 28.70 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.18), residues: 1833 helix: -1.37 (0.20), residues: 541 sheet: -2.38 (0.28), residues: 280 loop : -3.15 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 62 TYR 0.033 0.003 TYR C 167 PHE 0.045 0.003 PHE N 72 TRP 0.047 0.004 TRP Q 72 HIS 0.012 0.003 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.35 (51060) covalent geometry : angle 1.50891 / 0.60 (76625) hydrogen bonds : bond 0.12146 / 6.32 ( 1509) hydrogen bonds : angle 4.50974 / 1.79 ( 2948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 290 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6437 (pptt) REVERT: C 52 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7584 (p) REVERT: C 74 ILE cc_start: 0.7879 (tp) cc_final: 0.7593 (tp) REVERT: D 94 GLU cc_start: 0.7356 (tp30) cc_final: 0.6706 (tp30) REVERT: D 135 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7088 (tm-30) REVERT: D 170 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7348 (pp) REVERT: E 70 MET cc_start: 0.6927 (tpp) cc_final: 0.6543 (tpp) REVERT: F 4 TYR cc_start: -0.1579 (OUTLIER) cc_final: -0.3329 (m-80) REVERT: F 90 MET cc_start: 0.3468 (mmt) cc_final: 0.2840 (mmt) REVERT: H 9 MET cc_start: 0.4985 (tpp) cc_final: 0.4417 (tpp) REVERT: J 56 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.4712 (t-90) REVERT: J 62 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6316 (mtm110) REVERT: J 97 ASP cc_start: 0.2851 (p0) cc_final: 0.2564 (p0) REVERT: K 84 MET cc_start: 0.5743 (ttm) cc_final: 0.5355 (ptm) REVERT: N 22 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6997 (ptpp) REVERT: N 58 ARG cc_start: 0.6645 (mtt90) cc_final: 0.6389 (ttm170) REVERT: N 60 ARG cc_start: 0.4856 (pmt170) cc_final: 0.3572 (tpp-160) REVERT: P 34 GLU cc_start: 0.8029 (pm20) cc_final: 0.7821 (pm20) REVERT: Q 37 ILE cc_start: 0.7023 (tp) cc_final: 0.6795 (tp) REVERT: R 62 ARG cc_start: 0.3731 (tpp80) cc_final: 0.2649 (mtt180) REVERT: S 12 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6041 (pp) REVERT: S 64 GLU cc_start: 0.2473 (OUTLIER) cc_final: 0.1847 (tt0) REVERT: T 51 ASN cc_start: 0.7955 (m-40) cc_final: 0.7544 (m110) REVERT: T 58 ASP cc_start: 0.8941 (m-30) cc_final: 0.8693 (m-30) outliers start: 102 outliers final: 74 residues processed: 354 average time/residue: 0.3090 time to fit residues: 174.9287 Evaluate side-chains 366 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 69 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 107 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 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 = 0.4214 r_free = 0.4214 target = 0.153283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.145367 restraints weight = 168681.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.147280 restraints weight = 70702.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.148413 restraints weight = 36831.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.149105 restraints weight = 22665.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.149515 restraints weight = 16089.426| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.8426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 51060 Z= 0.428 Angle : 1.676 17.817 76625 Z= 0.666 Chirality : 0.118 1.558 9855 Planarity : 0.009 0.153 4028 Dihedral : 20.373 178.423 20462 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.35 % Favored : 82.60 % Rotamer: Outliers : 7.40 % Allowed : 29.14 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.28 % 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: -4.16 (0.17), residues: 1833 helix: -1.69 (0.20), residues: 531 sheet: -2.77 (0.27), residues: 297 loop : -3.48 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 25 TYR 0.039 0.004 TYR C 167 PHE 0.045 0.004 PHE N 72 TRP 0.053 0.005 TRP C 17 HIS 0.016 0.003 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.43 (51060) covalent geometry : angle 1.67580 / 0.67 (76625) hydrogen bonds : bond 0.13589 / 7.11 ( 1509) hydrogen bonds : angle 4.89708 / 1.94 ( 2948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 291 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6393 (pptt) REVERT: C 52 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7582 (p) REVERT: C 74 ILE cc_start: 0.7828 (tp) cc_final: 0.7553 (tp) REVERT: D 94 GLU cc_start: 0.7506 (tp30) cc_final: 0.6752 (tp30) REVERT: D 135 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7246 (tm-30) REVERT: E 70 MET cc_start: 0.6684 (tpp) cc_final: 0.6349 (tpp) REVERT: F 4 TYR cc_start: -0.1125 (OUTLIER) cc_final: -0.2500 (m-80) REVERT: J 56 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.4873 (t-90) REVERT: J 62 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6264 (mtm110) REVERT: L 82 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8016 (ttp80) REVERT: N 22 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6875 (ptpp) REVERT: N 52 ARG cc_start: 0.4108 (mmt180) cc_final: 0.3146 (mtt180) REVERT: N 58 ARG cc_start: 0.6463 (mtt90) cc_final: 0.6143 (ttm170) REVERT: N 60 ARG cc_start: 0.5253 (pmt170) cc_final: 0.4070 (tpp-160) REVERT: Q 80 LYS cc_start: 0.6943 (pptt) cc_final: 0.6733 (pptt) REVERT: R 62 ARG cc_start: 0.3634 (tpp80) cc_final: 0.2765 (mtt180) REVERT: S 12 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6016 (pp) REVERT: T 27 MET cc_start: 0.7724 (ttm) cc_final: 0.7496 (mtt) REVERT: T 58 ASP cc_start: 0.8976 (m-30) cc_final: 0.8745 (m-30) outliers start: 100 outliers final: 78 residues processed: 357 average time/residue: 0.3121 time to fit residues: 177.8801 Evaluate side-chains 364 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 28 ASN Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 95 optimal weight: 8.9990 chunk 218 optimal weight: 0.0470 chunk 33 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 327 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS E 77 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.158222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149538 restraints weight = 166309.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.151713 restraints weight = 69100.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.153003 restraints weight = 35477.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.153800 restraints weight = 21452.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.154295 restraints weight = 14896.497| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 51060 Z= 0.240 Angle : 1.305 17.375 76625 Z= 0.520 Chirality : 0.096 1.446 9855 Planarity : 0.006 0.063 4028 Dihedral : 19.831 179.662 20462 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 5.55 % Allowed : 31.51 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.18), residues: 1833 helix: -1.01 (0.21), residues: 530 sheet: -2.43 (0.28), residues: 293 loop : -3.27 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG T 59 TYR 0.029 0.002 TYR L 94 PHE 0.047 0.003 PHE N 72 TRP 0.037 0.003 TRP D 169 HIS 0.010 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (51060) covalent geometry : angle 1.30461 / 0.52 (76625) hydrogen bonds : bond 0.09874 / 5.21 ( 1509) hydrogen bonds : angle 4.17538 / 1.67 ( 2948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 286 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6579 (pptt) REVERT: C 52 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7386 (p) REVERT: C 74 ILE cc_start: 0.7657 (tp) cc_final: 0.7305 (tp) REVERT: D 94 GLU cc_start: 0.7234 (tp30) cc_final: 0.6710 (tp30) REVERT: D 135 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7090 (tm-30) REVERT: E 70 MET cc_start: 0.6904 (tpp) cc_final: 0.6458 (tpp) REVERT: F 4 TYR cc_start: -0.1603 (OUTLIER) cc_final: -0.3465 (m-80) REVERT: F 9 MET cc_start: 0.7964 (pmm) cc_final: 0.7672 (pmm) REVERT: H 9 MET cc_start: 0.4544 (tpp) cc_final: 0.4042 (tpp) REVERT: J 25 ILE cc_start: 0.7352 (pt) cc_final: 0.6838 (mm) REVERT: J 56 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.4679 (t-90) REVERT: J 62 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6049 (mtm110) REVERT: J 97 ASP cc_start: 0.3380 (p0) cc_final: 0.3016 (p0) REVERT: K 39 ASN cc_start: 0.6228 (m-40) cc_final: 0.5573 (t0) REVERT: N 58 ARG cc_start: 0.6604 (mtt90) cc_final: 0.6173 (tpp80) REVERT: N 80 ARG cc_start: 0.7640 (tmm-80) cc_final: 0.7338 (tmm-80) REVERT: P 34 GLU cc_start: 0.8032 (pm20) cc_final: 0.7779 (pm20) REVERT: R 62 ARG cc_start: 0.3666 (tpp80) cc_final: 0.2668 (mtt180) REVERT: S 12 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6173 (pp) REVERT: S 64 GLU cc_start: 0.2470 (OUTLIER) cc_final: 0.2017 (tt0) outliers start: 75 outliers final: 60 residues processed: 330 average time/residue: 0.3123 time to fit residues: 164.3228 Evaluate side-chains 340 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 273 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 28 ASN Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 29 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 34 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 HIS ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.157949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149333 restraints weight = 165924.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.151485 restraints weight = 68848.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.152765 restraints weight = 35383.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.153553 restraints weight = 21401.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.154047 restraints weight = 14862.612| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.8191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 51060 Z= 0.291 Angle : 1.345 59.200 76625 Z= 0.556 Chirality : 0.097 1.448 9855 Planarity : 0.006 0.106 4028 Dihedral : 19.832 179.657 20462 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer: Outliers : 5.62 % Allowed : 31.58 % Favored : 62.80 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.18), residues: 1833 helix: -1.03 (0.21), residues: 537 sheet: -2.45 (0.28), residues: 296 loop : -3.25 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 10 TYR 0.025 0.002 TYR L 94 PHE 0.043 0.003 PHE N 72 TRP 0.031 0.003 TRP D 169 HIS 0.009 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.29 (51060) covalent geometry : angle 1.34532 / 0.56 (76625) hydrogen bonds : bond 0.09959 / 5.25 ( 1509) hydrogen bonds : angle 4.17579 / 1.67 ( 2948) =============================================================================== Job complete usr+sys time: 8338.63 seconds wall clock time: 145 minutes 20.72 seconds (8720.72 seconds total)