Starting phenix.real_space_refine on Thu Dec 26 10:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6k_21558/12_2024/6w6k_21558.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6k_21558/12_2024/6w6k_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_21558/12_2024/6w6k_21558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6k_21558/12_2024/6w6k_21558.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6k_21558/12_2024/6w6k_21558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6k_21558/12_2024/6w6k_21558.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 19} 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: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 15} 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: 25.59, per 1000 atoms: 0.55 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: 12.10 Conformation dependent library (CDL) restraints added in 2.8 seconds 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 34.2% alpha, 11.0% beta 434 base pairs and 779 stacking pairs defined. Time for finding SS restraints: 21.70 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: 49.75 Time building geometry restraints manager: 14.03 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: 1.520 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: 0.050 Extract box with map and model: 1.890 Check model and map are aligned: 0.320 Set scattering table: 0.450 Process input model: 138.350 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.460 ------------------------------------------------------------------------------- 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= 0.102 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP C 166 HIS 0.005 0.001 HIS J 15 PHE 0.011 0.001 PHE S 9 TYR 0.017 0.001 TYR D 3 ARG 0.002 0.000 ARG D 62 *********************** 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 : 2.675 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: 0.7361 (tm-30) REVERT: D 88 ASN cc_start: 0.5746 (t0) cc_final: 0.5507 (t0) REVERT: E 151 MET cc_start: 0.4923 (mmm) cc_final: 0.4565 (ttm) REVERT: J 80 THR cc_start: 0.3416 (p) cc_final: 0.3073 (p) REVERT: N 60 ARG cc_start: 0.4010 (pmt170) cc_final: 0.3542 (tpp-160) REVERT: P 52 LEU cc_start: 0.6490 (mp) cc_final: 0.6286 (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: 0.8138 time to fit residues: 567.7604 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 : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 191 optimal weight: 0.0040 chunk 298 optimal weight: 6.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- 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 ** 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 L 72 ASN ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 70 HIS O 36 ASN O 41 HIS O 61 GLN ** 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 51060 Z= 0.257 Angle : 0.686 11.072 76625 Z= 0.343 Chirality : 0.036 0.245 9855 Planarity : 0.005 0.062 4028 Dihedral : 23.785 177.348 26020 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.40 % Allowed : 17.46 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.17), residues: 1833 helix: -1.58 (0.20), residues: 536 sheet: -2.34 (0.27), residues: 312 loop : -3.09 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP K 43 HIS 0.011 0.002 HIS S 13 PHE 0.027 0.002 PHE Q 27 TYR 0.019 0.002 TYR J 65 ARG 0.010 0.001 ARG H 83 *********************** 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 374 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 2.603 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: D 131 ILE cc_start: 0.7989 (mp) cc_final: 0.7639 (mt) REVERT: D 140 ASP cc_start: 0.6727 (m-30) cc_final: 0.6499 (m-30) REVERT: F 9 MET cc_start: 0.7734 (ptp) cc_final: 0.7463 (pmm) REVERT: N 8 ARG cc_start: 0.4952 (mmt180) cc_final: 0.4422 (mmt90) REVERT: N 60 ARG cc_start: 0.5173 (pmt170) cc_final: 0.4575 (tpm170) REVERT: O 58 MET cc_start: 0.6567 (mmm) cc_final: 0.6361 (mmm) REVERT: P 31 ARG cc_start: 0.8352 (tpt-90) cc_final: 0.8117 (ttt180) REVERT: P 70 ARG cc_start: 0.7748 (tpt-90) cc_final: 0.7384 (tpt170) REVERT: R 32 ILE cc_start: 0.5465 (mm) cc_final: 0.5096 (mm) outliers start: 46 outliers final: 31 residues processed: 352 average time/residue: 0.7811 time to fit residues: 433.6185 Evaluate side-chains 310 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ASN 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 D residue 33 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 30 ILE 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 54 LEU Chi-restraints excluded: chain P residue 55 ASP 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 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 166 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 299 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 chunk 266 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 77 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN K 14 GLN K 23 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN N 61 ASN O 41 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN S 13 HIS ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 51060 Z= 0.181 Angle : 0.606 11.085 76625 Z= 0.306 Chirality : 0.034 0.251 9855 Planarity : 0.004 0.046 4028 Dihedral : 23.684 178.844 26020 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.81 % Allowed : 19.97 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.18), residues: 1833 helix: -0.96 (0.22), residues: 543 sheet: -2.16 (0.27), residues: 316 loop : -2.87 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 41 HIS 0.014 0.001 HIS K 23 PHE 0.013 0.002 PHE N 72 TYR 0.012 0.002 TYR C 192 ARG 0.013 0.001 ARG N 40 *********************** 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 370 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 2.777 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: C 139 ASN cc_start: 0.6872 (m-40) cc_final: 0.6508 (m-40) REVERT: C 149 LYS cc_start: 0.5949 (tptt) cc_final: 0.5385 (tptt) REVERT: D 131 ILE cc_start: 0.8114 (mp) cc_final: 0.7747 (mt) REVERT: J 81 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7093 (tp30) REVERT: N 42 ASN cc_start: 0.5629 (OUTLIER) cc_final: 0.4990 (t0) REVERT: O 58 MET cc_start: 0.6677 (mmm) cc_final: 0.6403 (mmm) REVERT: P 70 ARG cc_start: 0.7642 (tpt-90) cc_final: 0.7391 (tpp80) REVERT: R 32 ILE cc_start: 0.5776 (mm) cc_final: 0.5525 (mm) REVERT: S 14 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6204 (pp) outliers start: 65 outliers final: 34 residues processed: 342 average time/residue: 0.7254 time to fit residues: 391.0613 Evaluate side-chains 311 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 9 GLU 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 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain O residue 11 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 S residue 14 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 300 optimal weight: 0.0770 chunk 318 optimal weight: 0.1980 chunk 156 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 18 ASN E 77 ASN E 121 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN L 95 HIS N 59 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN S 13 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 51060 Z= 0.159 Angle : 0.591 10.681 76625 Z= 0.297 Chirality : 0.033 0.298 9855 Planarity : 0.004 0.058 4028 Dihedral : 23.628 177.653 26020 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.66 % Allowed : 21.82 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.18), residues: 1833 helix: -0.56 (0.22), residues: 545 sheet: -1.86 (0.28), residues: 310 loop : -2.76 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 72 HIS 0.024 0.002 HIS K 23 PHE 0.021 0.002 PHE C 202 TYR 0.015 0.001 TYR D 50 ARG 0.012 0.001 ARG Q 61 *********************** 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 354 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 ARG cc_start: 0.5636 (ttt180) cc_final: 0.5074 (ptm160) REVERT: D 131 ILE cc_start: 0.7936 (mp) cc_final: 0.7613 (mt) REVERT: E 152 VAL cc_start: 0.6196 (t) cc_final: 0.5914 (t) REVERT: J 97 ASP cc_start: 0.1556 (p0) cc_final: 0.1262 (p0) REVERT: P 70 ARG cc_start: 0.7685 (tpt-90) cc_final: 0.7289 (tpp80) REVERT: S 12 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5432 (pp) REVERT: S 14 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6416 (pp) outliers start: 63 outliers final: 39 residues processed: 329 average time/residue: 0.6986 time to fit residues: 367.0211 Evaluate side-chains 310 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 154 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 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 26 MET 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 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU 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 66 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 20 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS K 23 HIS K 28 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 72 ASN L 95 HIS N 42 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 51060 Z= 0.229 Angle : 0.708 13.011 76625 Z= 0.358 Chirality : 0.038 0.305 9855 Planarity : 0.006 0.092 4028 Dihedral : 23.893 178.230 26020 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 5.55 % Allowed : 22.56 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.18), residues: 1833 helix: -0.75 (0.21), residues: 564 sheet: -1.96 (0.27), residues: 311 loop : -2.83 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 169 HIS 0.010 0.002 HIS J 15 PHE 0.016 0.002 PHE S 40 TYR 0.015 0.002 TYR E 49 ARG 0.023 0.001 ARG C 106 *********************** 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 376 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 2.637 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 130 ARG cc_start: 0.5941 (ttt180) cc_final: 0.5335 (ptm160) REVERT: C 149 LYS cc_start: 0.6097 (tptt) cc_final: 0.5828 (tptt) REVERT: H 2 MET cc_start: 0.4142 (ttt) cc_final: 0.3609 (tpt) REVERT: H 84 ILE cc_start: 0.7124 (mp) cc_final: 0.6893 (mt) REVERT: L 24 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5519 (mp0) REVERT: P 70 ARG cc_start: 0.7883 (tpt-90) cc_final: 0.7535 (tpt170) REVERT: R 51 GLN cc_start: 0.5455 (OUTLIER) cc_final: 0.5109 (pp30) REVERT: S 12 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5381 (pp) outliers start: 75 outliers final: 49 residues processed: 351 average time/residue: 0.7195 time to fit residues: 396.9036 Evaluate side-chains 334 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 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 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 7 VAL Chi-restraints excluded: chain F residue 75 GLU 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 128 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 32 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 73 VAL 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 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 O residue 11 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain S residue 12 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 chunk 264 optimal weight: 0.0980 chunk 147 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** K 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN S 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 51060 Z= 0.170 Angle : 0.623 13.237 76625 Z= 0.316 Chirality : 0.035 0.267 9855 Planarity : 0.005 0.064 4028 Dihedral : 23.785 177.435 26020 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.10 % Allowed : 25.30 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.19), residues: 1833 helix: -0.34 (0.22), residues: 547 sheet: -1.86 (0.28), residues: 304 loop : -2.63 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 169 HIS 0.041 0.002 HIS K 23 PHE 0.037 0.002 PHE N 72 TYR 0.034 0.002 TYR C 192 ARG 0.008 0.001 ARG K 97 *********************** 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 373 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 304 time to evaluate : 2.919 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: 0.5028 (p0) cc_final: 0.4791 (p0) REVERT: C 130 ARG cc_start: 0.5879 (ttt180) cc_final: 0.5236 (ptm160) REVERT: D 170 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6612 (pp) REVERT: F 75 GLU cc_start: 0.0479 (OUTLIER) cc_final: -0.0212 (tt0) REVERT: H 124 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.4936 (mm) REVERT: K 109 ILE cc_start: 0.8204 (mt) cc_final: 0.7949 (mt) REVERT: L 24 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5471 (mp0) REVERT: O 58 MET cc_start: 0.6792 (mmm) cc_final: 0.6513 (mmp) REVERT: P 70 ARG cc_start: 0.7808 (tpt-90) cc_final: 0.7385 (tpp80) REVERT: Q 29 LYS cc_start: 0.6179 (mmmt) cc_final: 0.5532 (ttpp) REVERT: R 51 GLN cc_start: 0.4743 (OUTLIER) cc_final: 0.4538 (pm20) REVERT: S 12 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5327 (pp) outliers start: 69 outliers final: 43 residues processed: 347 average time/residue: 0.7348 time to fit residues: 400.3376 Evaluate side-chains 322 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 HIS 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 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 73 VAL 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 48 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU 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 51 GLN Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 60 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 317 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN N 65 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 51060 Z= 0.144 Angle : 0.590 12.058 76625 Z= 0.298 Chirality : 0.033 0.237 9855 Planarity : 0.005 0.118 4028 Dihedral : 23.698 177.112 26020 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.51 % Allowed : 26.18 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.19), residues: 1833 helix: -0.14 (0.22), residues: 549 sheet: -1.67 (0.29), residues: 287 loop : -2.51 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 169 HIS 0.008 0.001 HIS O 41 PHE 0.033 0.002 PHE N 72 TYR 0.021 0.001 TYR C 41 ARG 0.015 0.001 ARG J 72 *********************** 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 357 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 2.630 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 130 ARG cc_start: 0.5774 (ttt180) cc_final: 0.5113 (ptm160) REVERT: C 149 LYS cc_start: 0.5985 (tptt) cc_final: 0.5763 (tptt) REVERT: D 170 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6569 (pp) REVERT: F 75 GLU cc_start: 0.0337 (OUTLIER) cc_final: -0.0272 (tt0) REVERT: H 124 ILE cc_start: 0.5351 (OUTLIER) cc_final: 0.4994 (mm) REVERT: J 97 ASP cc_start: 0.2819 (p0) cc_final: 0.2402 (p0) REVERT: L 66 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6168 (mt) REVERT: O 58 MET cc_start: 0.6762 (mmm) cc_final: 0.6464 (mmp) REVERT: P 70 ARG cc_start: 0.7732 (tpt-90) cc_final: 0.7327 (tpp80) REVERT: Q 57 VAL cc_start: 0.8345 (p) cc_final: 0.8038 (p) REVERT: S 12 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5535 (pp) outliers start: 61 outliers final: 49 residues processed: 331 average time/residue: 0.7007 time to fit residues: 364.2805 Evaluate side-chains 329 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 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 197 HIS 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 7 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 73 VAL 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 48 LEU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU 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 44 ILE 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 26 MET Chi-restraints excluded: chain T residue 67 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 189 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN L 72 ASN N 48 GLN N 65 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 51060 Z= 0.361 Angle : 0.941 17.039 76625 Z= 0.470 Chirality : 0.048 0.283 9855 Planarity : 0.007 0.104 4028 Dihedral : 24.551 179.912 26020 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.86 % Favored : 86.09 % Rotamer: Outliers : 5.84 % Allowed : 26.18 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.18), residues: 1833 helix: -1.18 (0.20), residues: 555 sheet: -2.29 (0.27), residues: 302 loop : -2.92 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 169 HIS 0.041 0.003 HIS S 13 PHE 0.030 0.003 PHE C 202 TYR 0.026 0.003 TYR C 192 ARG 0.017 0.001 ARG O 83 *********************** 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 376 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 2.643 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: 0.6126 (OUTLIER) cc_final: 0.5825 (pptt) REVERT: C 130 ARG cc_start: 0.6090 (ttt180) cc_final: 0.5423 (ptm160) REVERT: C 151 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6295 (tm-30) REVERT: D 170 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6921 (pp) REVERT: E 150 GLU cc_start: 0.6277 (mp0) cc_final: 0.6014 (mp0) REVERT: F 4 TYR cc_start: -0.1534 (OUTLIER) cc_final: -0.2943 (m-80) REVERT: H 124 ILE cc_start: 0.5662 (mm) cc_final: 0.5357 (mt) REVERT: K 13 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7025 (mmmt) REVERT: L 66 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6240 (mt) REVERT: O 58 MET cc_start: 0.6966 (mmm) cc_final: 0.6719 (mmp) REVERT: O 84 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6747 (mm) REVERT: P 70 ARG cc_start: 0.7938 (tpt-90) cc_final: 0.7539 (tpt170) REVERT: Q 29 LYS cc_start: 0.6299 (mmmt) cc_final: 0.5930 (ptmt) REVERT: Q 36 PHE cc_start: 0.5272 (m-80) cc_final: 0.5059 (m-10) REVERT: R 62 ARG cc_start: 0.4401 (tpp80) cc_final: 0.3233 (mtt180) outliers start: 79 outliers final: 56 residues processed: 343 average time/residue: 0.6903 time to fit residues: 377.8198 Evaluate side-chains 340 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ASN 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 123 LEU Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 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 170 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU 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 66 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 10 ARG Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 57 VAL 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 13 HIS Chi-restraints excluded: chain S residue 44 ILE 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 62 THR Chi-restraints excluded: chain S residue 65 MET 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 288 optimal weight: 0.9980 chunk 303 optimal weight: 9.9990 chunk 277 optimal weight: 30.0000 chunk 295 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 279 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 51060 Z= 0.216 Angle : 0.726 15.749 76625 Z= 0.368 Chirality : 0.039 0.246 9855 Planarity : 0.005 0.073 4028 Dihedral : 24.204 178.827 26020 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.59 % Allowed : 28.92 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.18), residues: 1833 helix: -0.91 (0.21), residues: 561 sheet: -2.37 (0.27), residues: 301 loop : -2.92 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 72 HIS 0.010 0.002 HIS O 41 PHE 0.033 0.002 PHE N 72 TYR 0.019 0.002 TYR C 192 ARG 0.007 0.001 ARG Q 10 *********************** 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 354 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5839 (pptt) REVERT: C 130 ARG cc_start: 0.5876 (ttt180) cc_final: 0.5231 (ptm160) REVERT: D 135 GLN cc_start: 0.7232 (tm-30) cc_final: 0.6900 (tm-30) REVERT: D 170 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6856 (pp) REVERT: E 19 ARG cc_start: 0.7886 (tpt170) cc_final: 0.7652 (tpt170) REVERT: F 4 TYR cc_start: -0.1532 (OUTLIER) cc_final: -0.3159 (m-80) REVERT: H 9 MET cc_start: 0.4534 (tpp) cc_final: 0.3991 (tpp) REVERT: J 97 ASP cc_start: 0.2956 (p0) cc_final: 0.2755 (p0) REVERT: L 66 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6116 (mt) REVERT: N 80 ARG cc_start: 0.7376 (tmm-80) cc_final: 0.6862 (tmm-80) REVERT: O 84 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6632 (mm) REVERT: P 70 ARG cc_start: 0.7845 (tpt-90) cc_final: 0.7493 (tpt170) REVERT: Q 29 LYS cc_start: 0.6357 (mmmt) cc_final: 0.5850 (ptmt) outliers start: 62 outliers final: 46 residues processed: 327 average time/residue: 0.7183 time to fit residues: 371.3778 Evaluate side-chains 327 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 276 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 94 GLU 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 E residue 29 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 71 LEU 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 66 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 10 ARG 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 R residue 39 VAL Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 60 PHE Chi-restraints excluded: chain T residue 26 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** H 15 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 51060 Z= 0.283 Angle : 0.811 18.966 76625 Z= 0.408 Chirality : 0.042 0.262 9855 Planarity : 0.006 0.080 4028 Dihedral : 24.409 178.657 26020 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.86 % Favored : 86.14 % Rotamer: Outliers : 4.22 % Allowed : 29.51 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.18), residues: 1833 helix: -0.96 (0.21), residues: 552 sheet: -2.36 (0.27), residues: 289 loop : -2.95 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP Q 72 HIS 0.012 0.002 HIS J 15 PHE 0.037 0.003 PHE C 202 TYR 0.024 0.002 TYR C 192 ARG 0.011 0.001 ARG D 62 ********************** 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 346 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 3.098 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: 0.6205 (OUTLIER) cc_final: 0.5896 (pptt) REVERT: C 130 ARG cc_start: 0.5978 (ttt180) cc_final: 0.5331 (ptm160) REVERT: D 135 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 170 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6988 (pp) REVERT: E 19 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7960 (tpt170) REVERT: H 9 MET cc_start: 0.4574 (tpp) cc_final: 0.4166 (tpp) REVERT: J 97 ASP cc_start: 0.2875 (p0) cc_final: 0.2633 (p0) REVERT: N 80 ARG cc_start: 0.7498 (tmm-80) cc_final: 0.7100 (tmm-80) REVERT: O 84 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6918 (mm) REVERT: P 70 ARG cc_start: 0.7890 (tpt-90) cc_final: 0.7488 (tpt170) REVERT: Q 29 LYS cc_start: 0.6623 (mmmt) cc_final: 0.6120 (ptmm) REVERT: R 62 ARG cc_start: 0.3792 (tpp80) cc_final: 0.2703 (mtt180) outliers start: 57 outliers final: 50 residues processed: 322 average time/residue: 0.7205 time to fit residues: 368.4340 Evaluate side-chains 335 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 TYR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 94 GLU 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 197 HIS 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 7 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 15 VAL 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 L residue 101 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 10 ARG 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 R residue 39 VAL Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 60 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- 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** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN K 23 HIS N 61 ASN P 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145515 restraints weight = 163440.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.147533 restraints weight = 68147.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.148722 restraints weight = 35272.496| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 51060 Z= 0.423 Angle : 1.057 20.426 76625 Z= 0.527 Chirality : 0.053 0.305 9855 Planarity : 0.007 0.085 4028 Dihedral : 25.051 179.399 26020 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.09 % Favored : 83.85 % Rotamer: Outliers : 5.40 % Allowed : 28.62 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 1.47 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.17), residues: 1833 helix: -1.56 (0.20), residues: 553 sheet: -2.51 (0.28), residues: 284 loop : -3.25 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP D 169 HIS 0.017 0.003 HIS J 15 PHE 0.029 0.004 PHE C 36 TYR 0.036 0.004 TYR C 192 ARG 0.010 0.001 ARG H 76 =============================================================================== Job complete usr+sys time: 7901.54 seconds wall clock time: 149 minutes 27.86 seconds (8967.86 seconds total)