Starting phenix.real_space_refine on Wed Aug 27 01:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6k_21558/08_2025/6w6k_21558.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6k_21558/08_2025/6w6k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6k_21558/08_2025/6w6k_21558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6k_21558/08_2025/6w6k_21558.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6k_21558/08_2025/6w6k_21558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6k_21558/08_2025/6w6k_21558.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 8.65, 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: 3.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 7.19 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: 20.90 Time building geometry restraints manager: 4.70 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=" O5' G A 803 " pdb=" C5' G A 803 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.59e+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 ... (remaining 51055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 76078 2.13 - 4.26: 487 4.26 - 6.40: 50 6.40 - 8.53: 8 8.53 - 10.66: 2 Bond angle restraints: 76625 Sorted by residual: angle pdb=" O3' G A 803 " pdb=" C3' G A 803 " pdb=" C2' G A 803 " ideal model delta sigma weight residual 113.70 107.49 6.21 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C3' U A1528 " pdb=" O3' U A1528 " pdb=" P G A1529 " ideal model delta sigma weight residual 120.20 125.77 -5.57 1.50e+00 4.44e-01 1.38e+01 angle pdb=" O3' U A1528 " pdb=" C3' U A1528 " pdb=" C2' U A1528 " ideal model delta sigma weight residual 109.50 115.02 -5.52 1.50e+00 4.44e-01 1.36e+01 angle pdb=" C3' A A1101 " pdb=" O3' A A1101 " pdb=" P A A1102 " ideal model delta sigma weight residual 120.20 125.60 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C3' U A1065 " pdb=" O3' U A1065 " pdb=" P C A1066 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 ... (remaining 76620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 28714 35.97 - 71.95: 3560 71.95 - 107.92: 422 107.92 - 143.90: 8 143.90 - 179.87: 10 Dihedral angle restraints: 32714 sinusoidal: 27362 harmonic: 5352 Sorted by residual: dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 41.70 158.30 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 48.88 151.12 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U A 4 " pdb=" C1' U A 4 " pdb=" N1 U A 4 " pdb=" C2 U A 4 " ideal model delta sinusoidal sigma weight residual 200.00 57.06 142.94 1 1.50e+01 4.44e-03 7.67e+01 ... (remaining 32711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 8855 0.043 - 0.086: 773 0.086 - 0.129: 180 0.129 - 0.171: 35 0.171 - 0.214: 12 Chirality restraints: 9855 Sorted by residual: chirality pdb=" C3' A A 802 " pdb=" C4' A A 802 " pdb=" O3' A A 802 " pdb=" C2' A A 802 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3' G A 484 " pdb=" C4' G A 484 " pdb=" O3' G A 484 " pdb=" C2' G A 484 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' U A1528 " pdb=" C4' U A1528 " pdb=" O3' U A1528 " pdb=" C2' U A1528 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.13e+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: 1.650 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 52.640 Find NCS groups from input model: 0.210 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: 0.020 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 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 : 0.002 0.046 51060 Z= 0.097 Angle : 0.467 10.661 76625 Z= 0.251 Chirality : 0.028 0.214 9855 Planarity : 0.003 0.028 4028 Dihedral : 23.244 179.873 29252 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 aren 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 covalent geometry : bond 0.00169 (51060) covalent geometry : angle 0.46699 (76625) hydrogen bonds : bond 0.11605 ( 1509) hydrogen bonds : angle 4.91005 ( 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 : 0.864 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: 0.6490 (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: 0.3439 time to fit residues: 240.0134 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 : 0.890 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 18 ASN C 24 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 197 HIS E 77 ASN E 134 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN H 117 GLN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 HIS K 27 ASN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 72 ASN ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 70 HIS O 41 HIS ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.166462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.156664 restraints weight = 166828.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.159034 restraints weight = 69937.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.160405 restraints weight = 35989.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.161213 restraints weight = 21945.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.161724 restraints weight = 15544.826| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 51060 Z= 0.282 Angle : 0.813 13.706 76625 Z= 0.405 Chirality : 0.042 0.258 9855 Planarity : 0.006 0.066 4028 Dihedral : 23.932 176.989 26020 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 4.51 % Allowed : 17.46 % Favored : 78.03 % 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 aren not related in a simple way. whole: -3.98 (0.17), residues: 1833 helix: -1.90 (0.19), residues: 555 sheet: -2.35 (0.26), residues: 317 loop : -3.28 (0.17), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 61 TYR 0.019 0.003 TYR E 49 PHE 0.032 0.003 PHE Q 27 TRP 0.027 0.004 TRP C 17 HIS 0.013 0.002 HIS S 13 Details of bonding type rmsd covalent geometry : bond 0.00547 (51060) covalent geometry : angle 0.81266 (76625) hydrogen bonds : bond 0.09830 ( 1509) hydrogen bonds : angle 3.91464 ( 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 390 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.758 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: C 32 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7853 (pp) REVERT: C 139 ASN cc_start: 0.7901 (m110) cc_final: 0.7633 (m-40) REVERT: D 70 GLN cc_start: 0.8243 (tt0) cc_final: 0.7931 (mt0) REVERT: D 94 GLU cc_start: 0.7494 (tp30) cc_final: 0.7189 (tp30) REVERT: E 110 MET cc_start: 0.5928 (pmm) cc_final: 0.5638 (pmm) REVERT: F 5 GLU cc_start: 0.6804 (mp0) cc_final: 0.6544 (mp0) REVERT: F 52 ASN cc_start: 0.5460 (t0) cc_final: 0.5184 (t0) REVERT: H 37 ASN cc_start: 0.7794 (m-40) cc_final: 0.7433 (m110) REVERT: N 8 ARG cc_start: 0.5675 (mmt180) cc_final: 0.5437 (mmt90) REVERT: N 60 ARG cc_start: 0.5426 (pmt170) cc_final: 0.4273 (tpp-160) REVERT: N 91 GLU cc_start: 0.7087 (tt0) cc_final: 0.6771 (tm-30) REVERT: P 31 ARG cc_start: 0.8537 (tpt-90) cc_final: 0.8308 (ttt180) REVERT: P 70 ARG cc_start: 0.7801 (tpt-90) cc_final: 0.7365 (tpp80) REVERT: S 14 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6361 (pp) outliers start: 61 outliers final: 37 residues processed: 359 average time/residue: 0.3267 time to fit residues: 182.3214 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 : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 138 GLN 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 60 VAL Chi-restraints excluded: chain D residue 106 PHE 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 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 F residue 75 GLU 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 K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 81 LEU 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 127 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 120 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN N 42 ASN N 48 GLN N 59 GLN N 61 ASN O 61 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN S 13 HIS T 69 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.161015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152227 restraints weight = 166365.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.154302 restraints weight = 69634.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.155516 restraints weight = 36074.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.156253 restraints weight = 22262.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.156709 restraints weight = 15887.202| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 51060 Z= 0.297 Angle : 0.906 17.926 76625 Z= 0.456 Chirality : 0.047 0.377 9855 Planarity : 0.008 0.106 4028 Dihedral : 24.438 178.927 26020 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 7.32 % Allowed : 21.82 % Favored : 70.86 % 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 aren not related in a simple way. whole: -3.90 (0.17), residues: 1833 helix: -1.64 (0.20), residues: 554 sheet: -2.37 (0.27), residues: 296 loop : -3.34 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 142 TYR 0.026 0.003 TYR C 167 PHE 0.022 0.003 PHE C 22 TRP 0.026 0.004 TRP N 41 HIS 0.050 0.003 HIS K 23 Details of bonding type rmsd covalent geometry : bond 0.00575 (51060) covalent geometry : angle 0.90577 (76625) hydrogen bonds : bond 0.11405 ( 1509) hydrogen bonds : angle 4.31690 ( 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 405 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 306 time to evaluate : 0.660 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: 0.5130 (OUTLIER) cc_final: 0.4669 (tt) REVERT: C 48 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6611 (pptt) REVERT: C 191 THR cc_start: 0.4712 (OUTLIER) cc_final: 0.4483 (t) REVERT: C 192 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.6017 (p90) REVERT: D 94 GLU cc_start: 0.7603 (tp30) cc_final: 0.7211 (tp30) REVERT: F 5 GLU cc_start: 0.6994 (mp0) cc_final: 0.6679 (mp0) REVERT: F 9 MET cc_start: 0.7937 (pmm) cc_final: 0.7585 (pmm) REVERT: J 81 GLU cc_start: 0.8016 (mm-30) cc_final: 0.6628 (mm-30) REVERT: K 36 ARG cc_start: 0.6250 (mtt180) cc_final: 0.6007 (mtt180) REVERT: L 24 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5732 (mp0) REVERT: N 60 ARG cc_start: 0.4575 (pmt170) cc_final: 0.3792 (tpm170) REVERT: N 89 ARG cc_start: 0.7344 (ttm110) cc_final: 0.7132 (ttm110) REVERT: P 70 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7417 (tpp80) REVERT: Q 29 LYS cc_start: 0.6632 (mmmm) cc_final: 0.6203 (ptmt) REVERT: S 12 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5571 (pp) REVERT: S 14 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6342 (pp) REVERT: S 64 GLU cc_start: 0.2738 (OUTLIER) cc_final: 0.2452 (tt0) outliers start: 99 outliers final: 50 residues processed: 371 average time/residue: 0.2561 time to fit residues: 148.6938 Evaluate side-chains 326 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 191 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 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 9 GLU 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 H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 26 MET 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 K residue 30 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU 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 53 ASP Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 57 ILE 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 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 26 MET 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: 0.0670 chunk 102 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 overall best weight: 5.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 125 ASN E 77 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN L 95 HIS N 42 ASN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.156678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.148129 restraints weight = 166311.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.150143 restraints weight = 69880.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.151314 restraints weight = 36556.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.152050 restraints weight = 22710.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.152483 restraints weight = 16195.101| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 51060 Z= 0.335 Angle : 0.989 23.819 76625 Z= 0.493 Chirality : 0.050 0.297 9855 Planarity : 0.008 0.107 4028 Dihedral : 24.863 179.932 26020 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.38 % Favored : 84.56 % Rotamer: Outliers : 8.58 % Allowed : 25.37 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -4.00 (0.17), residues: 1833 helix: -1.72 (0.20), residues: 553 sheet: -2.68 (0.28), residues: 277 loop : -3.31 (0.17), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 97 TYR 0.032 0.003 TYR C 167 PHE 0.032 0.004 PHE N 72 TRP 0.042 0.004 TRP Q 72 HIS 0.019 0.003 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00638 (51060) covalent geometry : angle 0.98874 (76625) hydrogen bonds : bond 0.12389 ( 1509) hydrogen bonds : angle 4.56922 ( 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 429 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 313 time to evaluate : 0.868 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: C 48 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6414 (pptt) REVERT: C 191 THR cc_start: 0.4951 (OUTLIER) cc_final: 0.4673 (t) REVERT: C 192 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.5872 (p90) REVERT: D 34 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: D 135 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7122 (tm-30) REVERT: E 10 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8452 (pp) REVERT: E 53 ARG cc_start: 0.8539 (tpp-160) cc_final: 0.8154 (mtt90) REVERT: F 4 TYR cc_start: -0.1665 (OUTLIER) cc_final: -0.2488 (m-80) REVERT: F 5 GLU cc_start: 0.7151 (mp0) cc_final: 0.6657 (mp0) REVERT: F 9 MET cc_start: 0.7153 (pmm) cc_final: 0.6784 (pmm) REVERT: H 2 MET cc_start: 0.2963 (OUTLIER) cc_final: 0.1550 (tmm) REVERT: N 22 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6825 (ptpp) REVERT: N 60 ARG cc_start: 0.5721 (pmt170) cc_final: 0.4057 (tpm170) REVERT: P 70 ARG cc_start: 0.7728 (tpt-90) cc_final: 0.7393 (tpp80) REVERT: Q 80 LYS cc_start: 0.6908 (pptt) cc_final: 0.6635 (pptt) REVERT: R 62 ARG cc_start: 0.4079 (tpp80) cc_final: 0.2806 (mtt180) REVERT: S 12 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5834 (pp) REVERT: S 14 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6053 (pp) outliers start: 116 outliers final: 73 residues processed: 392 average time/residue: 0.2618 time to fit residues: 161.7380 Evaluate side-chains 365 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 282 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 63 ILE 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 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 100 VAL 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 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 10 LEU 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 63 MET 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 122 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 18 ILE 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 71 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET 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 101 LEU Chi-restraints excluded: chain N residue 22 LYS 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 45 GLU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 4 ILE 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 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 169 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 99 ASN E 77 ASN E 121 ASN H 37 ASN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN T 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.158017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.148985 restraints weight = 164137.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.151160 restraints weight = 67604.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.152439 restraints weight = 34489.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.153211 restraints weight = 21028.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.153664 restraints weight = 14834.106| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 51060 Z= 0.219 Angle : 0.776 13.971 76625 Z= 0.393 Chirality : 0.042 0.262 9855 Planarity : 0.006 0.095 4028 Dihedral : 24.579 178.260 26020 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 6.88 % Allowed : 28.48 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -3.64 (0.18), residues: 1833 helix: -1.32 (0.21), residues: 549 sheet: -2.54 (0.27), residues: 297 loop : -3.11 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 61 TYR 0.017 0.002 TYR C 167 PHE 0.039 0.003 PHE N 72 TRP 0.031 0.003 TRP Q 72 HIS 0.013 0.002 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00417 (51060) covalent geometry : angle 0.77624 (76625) hydrogen bonds : bond 0.09612 ( 1509) hydrogen bonds : angle 4.05252 ( 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 398 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 0.872 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 111 ASP cc_start: 0.6215 (p0) cc_final: 0.5840 (p0) REVERT: C 139 ASN cc_start: 0.7367 (m-40) cc_final: 0.7082 (m-40) REVERT: C 175 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5295 (t70) REVERT: C 191 THR cc_start: 0.4823 (OUTLIER) cc_final: 0.4581 (t) REVERT: C 192 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.5771 (p90) REVERT: D 58 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8604 (mm-40) REVERT: D 135 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7028 (tm-30) REVERT: E 10 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8452 (pp) REVERT: E 19 ARG cc_start: 0.8323 (tpt170) cc_final: 0.8051 (tpt170) REVERT: E 53 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8179 (mtt90) REVERT: F 4 TYR cc_start: -0.1870 (OUTLIER) cc_final: -0.2924 (m-80) REVERT: F 5 GLU cc_start: 0.6976 (mp0) cc_final: 0.6530 (mp0) REVERT: F 9 MET cc_start: 0.7261 (pmm) cc_final: 0.6956 (pmm) REVERT: H 2 MET cc_start: 0.2913 (OUTLIER) cc_final: 0.1416 (tmm) REVERT: H 9 MET cc_start: 0.4212 (tpp) cc_final: 0.3729 (tpp) REVERT: H 124 ILE cc_start: 0.4756 (mm) cc_final: 0.4555 (mt) REVERT: J 56 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.4493 (t-90) REVERT: K 13 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7646 (mmmt) REVERT: K 84 MET cc_start: 0.5872 (ttt) cc_final: 0.5551 (ptm) REVERT: N 58 ARG cc_start: 0.6314 (mtm-85) cc_final: 0.6049 (mtm-85) REVERT: N 60 ARG cc_start: 0.5489 (pmt170) cc_final: 0.4482 (tpm170) REVERT: P 70 ARG cc_start: 0.7770 (tpt-90) cc_final: 0.7381 (tpp80) REVERT: Q 29 LYS cc_start: 0.6776 (mmmm) cc_final: 0.6490 (mmmm) REVERT: Q 80 LYS cc_start: 0.6922 (pptt) cc_final: 0.6614 (pptt) REVERT: R 62 ARG cc_start: 0.3798 (tpp80) cc_final: 0.2785 (ptt180) REVERT: S 12 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6091 (pp) outliers start: 93 outliers final: 61 residues processed: 362 average time/residue: 0.2623 time to fit residues: 149.2071 Evaluate side-chains 348 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP 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 165 GLU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 TYR 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 139 ASN Chi-restraints excluded: chain D residue 154 VAL 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 9 GLU Chi-restraints excluded: chain E residue 10 LEU 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 63 ASN Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain H residue 2 MET 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 18 ILE 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 71 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 15 VAL 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 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 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 32 ILE 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 12 LEU Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 130 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 309 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 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** ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN T 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.155905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.147062 restraints weight = 166585.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149191 restraints weight = 68866.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150440 restraints weight = 35355.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151209 restraints weight = 21527.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.151661 restraints weight = 15141.660| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 51060 Z= 0.257 Angle : 0.837 16.792 76625 Z= 0.422 Chirality : 0.045 0.276 9855 Planarity : 0.006 0.109 4028 Dihedral : 24.708 178.423 26020 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.66 % Favored : 84.34 % Rotamer: Outliers : 7.99 % Allowed : 28.48 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -3.67 (0.18), residues: 1833 helix: -1.27 (0.21), residues: 545 sheet: -2.55 (0.28), residues: 284 loop : -3.19 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 58 TYR 0.030 0.002 TYR C 167 PHE 0.031 0.003 PHE N 72 TRP 0.032 0.003 TRP Q 72 HIS 0.013 0.002 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00493 (51060) covalent geometry : angle 0.83739 (76625) hydrogen bonds : bond 0.10597 ( 1509) hydrogen bonds : angle 4.20680 ( 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 400 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 292 time to evaluate : 0.778 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 111 ASP cc_start: 0.6010 (p0) cc_final: 0.5561 (p0) REVERT: C 191 THR cc_start: 0.4785 (OUTLIER) cc_final: 0.4524 (t) REVERT: C 192 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5867 (p90) REVERT: D 135 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7051 (tm-30) REVERT: E 10 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8430 (pp) REVERT: E 19 ARG cc_start: 0.8349 (tpt170) cc_final: 0.7918 (tpt170) REVERT: E 53 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8163 (mtt90) REVERT: F 4 TYR cc_start: -0.1533 (OUTLIER) cc_final: -0.2730 (m-80) REVERT: F 5 GLU cc_start: 0.7220 (mp0) cc_final: 0.6854 (mp0) REVERT: F 9 MET cc_start: 0.7264 (pmm) cc_final: 0.6899 (pmm) REVERT: F 90 MET cc_start: 0.3100 (mmt) cc_final: 0.2684 (mmt) REVERT: H 9 MET cc_start: 0.4422 (tpp) cc_final: 0.4195 (tpp) REVERT: J 11 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7774 (mmmm) REVERT: J 56 HIS cc_start: 0.6286 (OUTLIER) cc_final: 0.4745 (t-90) REVERT: N 60 ARG cc_start: 0.4864 (pmt170) cc_final: 0.4376 (tpm170) REVERT: O 46 LYS cc_start: 0.4342 (OUTLIER) cc_final: 0.2402 (tptp) REVERT: Q 29 LYS cc_start: 0.6719 (mmmm) cc_final: 0.6391 (mmmm) REVERT: Q 61 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7914 (ptp-170) REVERT: Q 80 LYS cc_start: 0.6995 (pptt) cc_final: 0.6751 (pptt) REVERT: R 62 ARG cc_start: 0.3799 (tpp80) cc_final: 0.2697 (mtt180) REVERT: S 12 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6055 (pp) outliers start: 108 outliers final: 77 residues processed: 361 average time/residue: 0.2671 time to fit residues: 153.8437 Evaluate side-chains 363 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 279 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 166 TRP 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 191 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 100 VAL 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 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 9 GLU Chi-restraints excluded: chain E residue 10 LEU 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 122 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 81 ASN 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 18 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 99 LEU 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 95 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 58 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 12 LEU Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 57 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 22 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 69 ASN 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: 9.9990 chunk 256 optimal weight: 0.2980 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 253 optimal weight: 0.2980 chunk 225 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 121 ASN H 15 ASN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN S 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.158950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.149876 restraints weight = 162747.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.152162 restraints weight = 66026.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.153489 restraints weight = 33308.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.154268 restraints weight = 20009.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.154797 restraints weight = 14054.534| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 51060 Z= 0.181 Angle : 0.721 16.061 76625 Z= 0.365 Chirality : 0.040 0.247 9855 Planarity : 0.005 0.079 4028 Dihedral : 24.466 178.169 26020 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 6.66 % Allowed : 30.55 % Favored : 62.80 % 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 aren not related in a simple way. whole: -3.45 (0.18), residues: 1833 helix: -0.98 (0.21), residues: 540 sheet: -2.60 (0.27), residues: 299 loop : -3.05 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 12 TYR 0.014 0.002 TYR C 167 PHE 0.033 0.002 PHE N 72 TRP 0.025 0.003 TRP D 169 HIS 0.012 0.002 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00346 (51060) covalent geometry : angle 0.72052 (76625) hydrogen bonds : bond 0.08634 ( 1509) hydrogen bonds : angle 3.90638 ( 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 384 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 294 time to evaluate : 0.874 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: 0.6873 (OUTLIER) cc_final: 0.6522 (pptt) REVERT: C 52 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.7926 (p) REVERT: C 111 ASP cc_start: 0.6430 (p0) cc_final: 0.6146 (p0) REVERT: C 191 THR cc_start: 0.4890 (OUTLIER) cc_final: 0.4634 (t) REVERT: D 58 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8655 (tm-30) REVERT: D 123 MET cc_start: 0.7779 (mmm) cc_final: 0.7487 (tpt) REVERT: D 135 GLN cc_start: 0.7556 (tm-30) cc_final: 0.6926 (tm-30) REVERT: E 19 ARG cc_start: 0.8385 (tpt170) cc_final: 0.7897 (tpt170) REVERT: E 53 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8088 (mtt90) REVERT: F 4 TYR cc_start: -0.1860 (OUTLIER) cc_final: -0.3212 (m-80) REVERT: F 5 GLU cc_start: 0.7314 (mp0) cc_final: 0.6799 (mp0) REVERT: F 9 MET cc_start: 0.7248 (pmm) cc_final: 0.6927 (pmm) REVERT: J 56 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.4591 (t-90) REVERT: J 81 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: K 84 MET cc_start: 0.5716 (ttt) cc_final: 0.5492 (ptm) REVERT: N 58 ARG cc_start: 0.6309 (mtm-85) cc_final: 0.5453 (tpp80) REVERT: O 46 LYS cc_start: 0.4047 (OUTLIER) cc_final: 0.1913 (tptp) REVERT: Q 29 LYS cc_start: 0.6708 (mmmm) cc_final: 0.6435 (mmmm) REVERT: Q 61 ARG cc_start: 0.8270 (ptp-170) cc_final: 0.8037 (ptp-170) REVERT: R 62 ARG cc_start: 0.3948 (tpp80) cc_final: 0.2944 (ptt180) REVERT: S 12 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6033 (pp) REVERT: S 64 GLU cc_start: 0.3076 (OUTLIER) cc_final: 0.2696 (tt0) REVERT: S 77 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.2348 (tpt170) outliers start: 90 outliers final: 58 residues processed: 354 average time/residue: 0.2875 time to fit residues: 161.6492 Evaluate side-chains 340 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 272 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 105 VAL 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 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 141 VAL 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 9 GLU Chi-restraints excluded: chain E residue 24 VAL 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 63 ASN 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 18 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 6 LEU 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 N residue 66 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 32 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 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 S residue 77 ARG Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 MET 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: 10.0000 chunk 161 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 77 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN S 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.153011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.144760 restraints weight = 166255.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146742 restraints weight = 69369.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.147908 restraints weight = 35946.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.148604 restraints weight = 22043.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.149063 restraints weight = 15682.863| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 51060 Z= 0.401 Angle : 1.061 16.979 76625 Z= 0.523 Chirality : 0.053 0.297 9855 Planarity : 0.008 0.104 4028 Dihedral : 25.074 178.902 26020 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.35 % Favored : 82.65 % Rotamer: Outliers : 8.36 % Allowed : 29.22 % Favored : 62.43 % 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 aren not related in a simple way. whole: -3.93 (0.17), residues: 1833 helix: -1.51 (0.20), residues: 534 sheet: -2.71 (0.27), residues: 307 loop : -3.31 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 178 TYR 0.034 0.003 TYR C 167 PHE 0.029 0.004 PHE N 72 TRP 0.025 0.003 TRP D 169 HIS 0.015 0.003 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00765 (51060) covalent geometry : angle 1.06061 (76625) hydrogen bonds : bond 0.13286 ( 1509) hydrogen bonds : angle 4.69403 ( 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 397 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 284 time to evaluate : 0.922 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: 0.6937 (OUTLIER) cc_final: 0.6490 (pptt) REVERT: C 133 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6734 (ttm) REVERT: D 8 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7872 (mp) REVERT: D 34 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: D 58 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8499 (tm-30) REVERT: D 135 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7138 (tm-30) REVERT: E 53 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8160 (mtt90) REVERT: F 4 TYR cc_start: -0.0317 (OUTLIER) cc_final: -0.1407 (m-80) REVERT: F 5 GLU cc_start: 0.7396 (mp0) cc_final: 0.6908 (mp0) REVERT: F 90 MET cc_start: 0.3121 (mmt) cc_final: 0.2754 (mmt) REVERT: H 9 MET cc_start: 0.5156 (tpp) cc_final: 0.4725 (tpp) REVERT: H 125 ILE cc_start: 0.5648 (OUTLIER) cc_final: 0.5397 (mp) REVERT: J 40 ILE cc_start: 0.6975 (pp) cc_final: 0.6356 (mm) REVERT: J 56 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.4703 (t-90) REVERT: K 23 HIS cc_start: 0.6205 (t-90) cc_final: 0.5921 (t-90) REVERT: N 22 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6929 (ptpp) REVERT: N 60 ARG cc_start: 0.5082 (pmt170) cc_final: 0.3995 (tpm170) REVERT: O 46 LYS cc_start: 0.4317 (OUTLIER) cc_final: 0.2354 (tptp) REVERT: P 34 GLU cc_start: 0.8127 (pm20) cc_final: 0.7915 (pm20) REVERT: Q 80 LYS cc_start: 0.6974 (pptt) cc_final: 0.6678 (pptt) REVERT: R 62 ARG cc_start: 0.3570 (tpp80) cc_final: 0.2665 (mtt180) REVERT: S 12 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6070 (pp) REVERT: S 77 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.2987 (tpt170) REVERT: T 51 ASN cc_start: 0.7633 (m-40) cc_final: 0.7346 (m110) outliers start: 113 outliers final: 83 residues processed: 359 average time/residue: 0.3072 time to fit residues: 174.2692 Evaluate side-chains 369 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 275 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 166 TRP Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 181 ILE 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 34 GLU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN 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 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 9 GLU Chi-restraints excluded: chain E residue 24 VAL 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 92 ARG 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 E residue 130 THR Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 81 ASN 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 125 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 ILE 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 71 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 6 LEU 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 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 46 LYS Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 32 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 13 HIS 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 S residue 77 ARG Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 107 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN K 14 GLN ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.153082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.144898 restraints weight = 164076.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.146911 restraints weight = 67879.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.148093 restraints weight = 34908.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.148809 restraints weight = 21294.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.149243 restraints weight = 14946.237| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 51060 Z= 0.346 Angle : 0.995 17.063 76625 Z= 0.497 Chirality : 0.051 0.312 9855 Planarity : 0.007 0.087 4028 Dihedral : 25.131 179.977 26020 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.58 % Favored : 83.42 % Rotamer: Outliers : 8.58 % Allowed : 29.66 % Favored : 61.76 % 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 aren not related in a simple way. whole: -4.08 (0.17), residues: 1833 helix: -1.56 (0.20), residues: 537 sheet: -2.84 (0.27), residues: 311 loop : -3.44 (0.17), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 12 TYR 0.031 0.003 TYR C 167 PHE 0.036 0.004 PHE N 72 TRP 0.029 0.003 TRP D 169 HIS 0.019 0.003 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00666 (51060) covalent geometry : angle 0.99527 (76625) hydrogen bonds : bond 0.12420 ( 1509) hydrogen bonds : angle 4.68416 ( 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 407 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 291 time to evaluate : 0.942 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 44 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7872 (mtmm) REVERT: C 48 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6381 (pptt) REVERT: C 133 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6795 (ttm) REVERT: C 141 MET cc_start: 0.6401 (ppp) cc_final: 0.6029 (tmm) REVERT: D 8 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8066 (mp) REVERT: D 34 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7146 (pt0) REVERT: D 135 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7131 (tm-30) REVERT: D 177 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7283 (ptm) REVERT: E 53 ARG cc_start: 0.8521 (tpp-160) cc_final: 0.8081 (mtt90) REVERT: E 70 MET cc_start: 0.6556 (tpp) cc_final: 0.6303 (tpp) REVERT: E 92 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.4329 (mmt180) REVERT: F 4 TYR cc_start: -0.0932 (OUTLIER) cc_final: -0.2360 (t80) REVERT: H 2 MET cc_start: 0.4271 (tmm) cc_final: 0.3795 (ttp) REVERT: H 9 MET cc_start: 0.4932 (tpp) cc_final: 0.4460 (tpp) REVERT: J 40 ILE cc_start: 0.6964 (pp) cc_final: 0.6457 (mm) REVERT: J 56 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.4644 (t-90) REVERT: J 81 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: J 97 ASP cc_start: 0.3648 (p0) cc_final: 0.3313 (p0) REVERT: N 22 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6975 (ptpp) REVERT: N 52 ARG cc_start: 0.4754 (mmt180) cc_final: 0.3744 (mtt180) REVERT: N 58 ARG cc_start: 0.6437 (mtt180) cc_final: 0.5782 (ttm170) REVERT: N 60 ARG cc_start: 0.4918 (pmt170) cc_final: 0.3678 (tpp-160) REVERT: P 34 GLU cc_start: 0.8130 (pm20) cc_final: 0.7895 (pm20) REVERT: Q 29 LYS cc_start: 0.6567 (mmmt) cc_final: 0.6090 (ptmm) REVERT: Q 72 TRP cc_start: 0.6481 (OUTLIER) cc_final: 0.5747 (m-90) REVERT: R 62 ARG cc_start: 0.3608 (tpp80) cc_final: 0.2744 (mtt180) REVERT: S 12 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.5775 (pp) outliers start: 116 outliers final: 82 residues processed: 368 average time/residue: 0.3034 time to fit residues: 178.4313 Evaluate side-chains 368 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 274 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 166 TRP 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 34 GLU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 100 VAL 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 170 LEU 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 9 GLU Chi-restraints excluded: chain E residue 24 VAL 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 92 ARG 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 4 TYR 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 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 18 ILE 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 71 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain K residue 32 THR 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 K residue 99 LEU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 23 LEU 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 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 59 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 72 TRP 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 13 HIS 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 12 GLN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 95 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 199 optimal weight: 0.0770 chunk 183 optimal weight: 0.0770 chunk 278 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 77 ASN H 15 ASN ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.150118 restraints weight = 164693.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.152224 restraints weight = 68394.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.153470 restraints weight = 35247.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.154222 restraints weight = 21414.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.154671 restraints weight = 14909.857| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.7854 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= 0.184 Angle : 0.769 16.552 76625 Z= 0.388 Chirality : 0.042 0.299 9855 Planarity : 0.006 0.091 4028 Dihedral : 24.678 179.322 26020 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % Rotamer: Outliers : 6.07 % Allowed : 32.03 % Favored : 61.91 % 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 aren not related in a simple way. whole: -3.54 (0.18), residues: 1833 helix: -1.07 (0.21), residues: 529 sheet: -2.45 (0.29), residues: 274 loop : -3.16 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 83 TYR 0.016 0.002 TYR D 75 PHE 0.042 0.003 PHE N 72 TRP 0.030 0.003 TRP C 17 HIS 0.013 0.002 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00355 (51060) covalent geometry : angle 0.76919 (76625) hydrogen bonds : bond 0.09100 ( 1509) hydrogen bonds : angle 4.07596 ( 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 371 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 289 time to evaluate : 0.902 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: 0.6814 (OUTLIER) cc_final: 0.6279 (pptt) REVERT: C 52 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8022 (p) REVERT: C 141 MET cc_start: 0.6476 (ppp) cc_final: 0.5994 (tmm) REVERT: D 123 MET cc_start: 0.7753 (mmm) cc_final: 0.7361 (tpt) REVERT: D 135 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 177 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6991 (ptm) REVERT: E 53 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8168 (mtt90) REVERT: F 4 TYR cc_start: -0.1058 (OUTLIER) cc_final: -0.2258 (t80) REVERT: H 9 MET cc_start: 0.4610 (tpp) cc_final: 0.4285 (tpp) REVERT: J 8 ILE cc_start: 0.6337 (mm) cc_final: 0.6133 (mm) REVERT: J 40 ILE cc_start: 0.6617 (pp) cc_final: 0.6230 (mm) REVERT: J 56 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.4812 (t-90) REVERT: J 97 ASP cc_start: 0.3369 (p0) cc_final: 0.3053 (p0) REVERT: K 23 HIS cc_start: 0.6437 (t-90) cc_final: 0.5980 (t-90) REVERT: P 34 GLU cc_start: 0.8149 (pm20) cc_final: 0.7893 (pm20) REVERT: Q 29 LYS cc_start: 0.6709 (mmmt) cc_final: 0.5869 (ttpp) REVERT: Q 32 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7558 (tp) REVERT: R 62 ARG cc_start: 0.3473 (tpp80) cc_final: 0.2498 (mtt180) REVERT: S 12 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.5733 (pp) outliers start: 82 outliers final: 66 residues processed: 337 average time/residue: 0.2996 time to fit residues: 162.5907 Evaluate side-chains 349 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 166 TRP 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 35 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 GLN 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 170 LEU 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 24 VAL 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 77 ASN 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 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 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 23 LEU 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 66 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 72 TRP 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 13 HIS 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 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: 10.0000 chunk 77 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.158241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.150023 restraints weight = 166116.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.152069 restraints weight = 69900.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.153282 restraints weight = 36319.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.154014 restraints weight = 22119.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154469 restraints weight = 15499.094| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.7870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 51060 Z= 0.242 Angle : 0.833 59.195 76625 Z= 0.437 Chirality : 0.043 0.319 9855 Planarity : 0.006 0.105 4028 Dihedral : 24.678 179.329 26020 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 6.29 % Allowed : 32.10 % Favored : 61.61 % 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 aren not related in a simple way. whole: -3.52 (0.18), residues: 1833 helix: -1.04 (0.21), residues: 529 sheet: -2.44 (0.29), residues: 274 loop : -3.15 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG S 54 TYR 0.016 0.002 TYR C 167 PHE 0.039 0.003 PHE N 72 TRP 0.025 0.003 TRP C 17 HIS 0.012 0.002 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00465 (51060) covalent geometry : angle 0.83302 (76625) hydrogen bonds : bond 0.09189 ( 1509) hydrogen bonds : angle 4.07622 ( 2948) =============================================================================== Job complete usr+sys time: 7489.44 seconds wall clock time: 130 minutes 49.40 seconds (7849.40 seconds total)