Starting phenix.real_space_refine on Tue Dec 31 02:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s9u_24937/12_2024/7s9u_24937.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9u_24937/12_2024/7s9u_24937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s9u_24937/12_2024/7s9u_24937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9u_24937/12_2024/7s9u_24937.map" model { file = "/net/cci-nas-00/data/ceres_data/7s9u_24937/12_2024/7s9u_24937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9u_24937/12_2024/7s9u_24937.cif" } resolution = 3.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2436 5.49 5 S 52 5.16 5 C 33528 2.51 5 N 12812 2.21 5 O 19792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.87s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 68620 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 52346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2436, 52346 Classifications: {'RNA': 2436} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 126, 'rna3p_pur': 1181, 'rna3p_pyr': 879} Link IDs: {'rna2p': 376, 'rna3p': 2059} Chain breaks: 5 Chain: "C" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2052 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1354 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 973 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 1 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 741 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "V" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Time building chain proxies: 28.11, per 1000 atoms: 0.41 Number of scatterers: 68620 At special positions: 0 Unit cell: (206.91, 196.65, 206.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 2436 15.00 O 19792 8.00 N 12812 7.00 C 33528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 33 " - pdb=" SG CYS b 46 " distance=2.04 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: 12.11 Conformation dependent library (CDL) restraints added in 2.2 seconds 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 33 sheets defined 24.1% alpha, 17.7% beta 697 base pairs and 1236 stacking pairs defined. Time for finding SS restraints: 23.60 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.675A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.156A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.849A pdb=" N SER D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.681A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 31 through 44 removed outlier: 3.894A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE E 37 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.887A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.656A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 3.874A pdb=" N SER J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 4.206A pdb=" N ILE J 63 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 72 Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.715A pdb=" N GLU J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 121 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 removed outlier: 3.694A pdb=" N SER K 116 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.529A pdb=" N LEU L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 removed outlier: 3.631A pdb=" N THR L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.672A pdb=" N LYS L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 4.002A pdb=" N LYS N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE N 25 " --> pdb=" O THR N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 52 removed outlier: 4.661A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS N 52 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 3.529A pdb=" N ARG N 59 " --> pdb=" O ASP N 55 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 86 removed outlier: 3.610A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 90 Processing helix chain 'P' and resid 6 through 10 Processing helix chain 'P' and resid 100 through 105 removed outlier: 3.699A pdb=" N LEU P 103 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 4.026A pdb=" N LYS Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG Q 13 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.058A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 57 removed outlier: 4.387A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN Q 38 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET Q 40 " --> pdb=" O ASN Q 36 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY Q 43 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN Q 44 " --> pdb=" O MET Q 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN Q 52 " --> pdb=" O ARG Q 48 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 69 removed outlier: 3.773A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 86 removed outlier: 3.914A pdb=" N GLY Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 118 removed outlier: 3.944A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.264A pdb=" N LEU S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.853A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 61 removed outlier: 3.506A pdb=" N ILE S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 Processing helix chain 'T' and resid 19 through 23 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.812A pdb=" N LYS T 40 " --> pdb=" O LYS T 36 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP T 41 " --> pdb=" O THR T 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.883A pdb=" N THR Z 22 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG Z 24 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 4.036A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 17 Processing helix chain 'Y' and resid 17 through 35 removed outlier: 3.714A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 61 removed outlier: 3.670A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 17 removed outlier: 3.890A pdb=" N VAL d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 3.641A pdb=" N GLY d 38 " --> pdb=" O ARG d 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.941A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.583A pdb=" N LEU C 165 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 7 removed outlier: 7.129A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.560A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP D 54 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N ASN D 33 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 120 removed outlier: 3.718A pdb=" N GLN D 120 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 13 through 17 removed outlier: 4.914A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 4 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 154 through 156 removed outlier: 6.092A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AB2, first strand: chain 'J' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 19 through 24 removed outlier: 7.113A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.443A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.975A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE L 111 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 124 through 125 Processing sheet with id=AB7, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.309A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU N 104 " --> pdb=" O MET N 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 71 through 74 Processing sheet with id=AB9, first strand: chain 'P' and resid 71 through 74 removed outlier: 6.770A pdb=" N THR P 63 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE P 67 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLU P 47 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.623A pdb=" N GLY R 66 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 58 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 71 through 77 removed outlier: 4.042A pdb=" N VAL R 82 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.673A pdb=" N LYS S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL S 107 " --> pdb=" O LYS S 4 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL S 6 " --> pdb=" O ILE S 105 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE S 105 " --> pdb=" O VAL S 6 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AC6, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.641A pdb=" N GLU T 29 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR T 27 " --> pdb=" O PRO T 11 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 63 through 66 removed outlier: 3.648A pdb=" N GLY T 71 " --> pdb=" O LYS T 64 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 33 through 35 removed outlier: 6.708A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY U 21 " --> pdb=" O VAL U 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL U 9 " --> pdb=" O GLY U 21 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 40 through 45 Processing sheet with id=AD1, first strand: chain 'U' and resid 81 through 85 Processing sheet with id=AD2, first strand: chain 'V' and resid 30 through 31 removed outlier: 7.219A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE V 68 " --> pdb=" O GLY V 60 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 38 through 39 Processing sheet with id=AD4, first strand: chain 'V' and resid 78 through 79 removed outlier: 3.573A pdb=" N LYS V 86 " --> pdb=" O GLU V 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AD6, first strand: chain 'b' and resid 27 through 29 400 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1775 hydrogen bonds 2952 hydrogen bond angles 0 basepair planarities 697 basepair parallelities 1236 stacking parallelities Total time for adding SS restraints: 82.92 Time building geometry restraints manager: 14.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6664 1.31 - 1.44: 34093 1.44 - 1.56: 29392 1.56 - 1.69: 4866 1.69 - 1.81: 97 Bond restraints: 75112 Sorted by residual: bond pdb=" CA ASN J 8 " pdb=" CB ASN J 8 " ideal model delta sigma weight residual 1.527 1.398 0.129 2.48e-02 1.63e+03 2.71e+01 bond pdb=" O3' G A 160 " pdb=" P A A 161 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.50e-02 4.44e+03 1.84e+01 bond pdb=" C LYS E 100 " pdb=" N LEU E 101 " ideal model delta sigma weight residual 1.333 1.236 0.096 2.74e-02 1.33e+03 1.24e+01 bond pdb=" O3' G A 26 " pdb=" P G A 27 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.13e+01 bond pdb=" O5' G A1512 " pdb=" C5' G A1512 " ideal model delta sigma weight residual 1.420 1.469 -0.049 1.50e-02 4.44e+03 1.08e+01 ... (remaining 75107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 112956 4.16 - 8.32: 545 8.32 - 12.48: 18 12.48 - 16.64: 4 16.64 - 20.79: 1 Bond angle restraints: 113524 Sorted by residual: angle pdb=" C3' C A1511 " pdb=" O3' C A1511 " pdb=" P G A1512 " ideal model delta sigma weight residual 120.20 135.86 -15.66 1.50e+00 4.44e-01 1.09e+02 angle pdb=" C3' G A 160 " pdb=" O3' G A 160 " pdb=" P A A 161 " ideal model delta sigma weight residual 120.20 133.25 -13.05 1.50e+00 4.44e-01 7.57e+01 angle pdb=" O3' G A 839 " pdb=" C3' G A 839 " pdb=" C2' G A 839 " ideal model delta sigma weight residual 109.50 121.32 -11.82 1.50e+00 4.44e-01 6.21e+01 angle pdb=" N VAL Q 90 " pdb=" CA VAL Q 90 " pdb=" C VAL Q 90 " ideal model delta sigma weight residual 108.12 97.90 10.22 1.34e+00 5.57e-01 5.82e+01 angle pdb=" O3' A A 161 " pdb=" C3' A A 161 " pdb=" C2' A A 161 " ideal model delta sigma weight residual 113.70 102.44 11.26 1.50e+00 4.44e-01 5.63e+01 ... (remaining 113519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 41702 35.92 - 71.84: 5710 71.84 - 107.76: 626 107.76 - 143.67: 46 143.67 - 179.59: 31 Dihedral angle restraints: 48115 sinusoidal: 42206 harmonic: 5909 Sorted by residual: dihedral pdb=" O4' U A 892 " pdb=" C1' U A 892 " pdb=" N1 U A 892 " pdb=" C2 U A 892 " ideal model delta sinusoidal sigma weight residual -160.00 16.67 -176.67 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 482 " pdb=" C1' C A 482 " pdb=" N1 C A 482 " pdb=" C2 C A 482 " ideal model delta sinusoidal sigma weight residual -160.00 16.16 -176.16 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 857 " pdb=" C1' U A 857 " pdb=" N1 U A 857 " pdb=" C2 U A 857 " ideal model delta sinusoidal sigma weight residual 200.00 24.61 175.39 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 48112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 14037 0.131 - 0.261: 595 0.261 - 0.392: 33 0.392 - 0.523: 1 0.523 - 0.654: 2 Chirality restraints: 14668 Sorted by residual: chirality pdb=" C3' G A 839 " pdb=" C4' G A 839 " pdb=" O3' G A 839 " pdb=" C2' G A 839 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C3' U A1595 " pdb=" C4' U A1595 " pdb=" O3' U A1595 " pdb=" C2' U A1595 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C1' G A1712 " pdb=" O4' G A1712 " pdb=" C2' G A1712 " pdb=" N9 G A1712 " both_signs ideal model delta sigma weight residual False 2.46 1.99 0.47 2.00e-01 2.50e+01 5.53e+00 ... (remaining 14665 not shown) Planarity restraints: 5269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " -0.098 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO R 51 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A1245 " 0.065 2.00e-02 2.50e+03 2.84e-02 2.43e+01 pdb=" N9 G A1245 " -0.070 2.00e-02 2.50e+03 pdb=" C8 G A1245 " -0.009 2.00e-02 2.50e+03 pdb=" N7 G A1245 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A1245 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A1245 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G A1245 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G A1245 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A1245 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A1245 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G A1245 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1245 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1026 " 0.051 2.00e-02 2.50e+03 2.39e-02 1.57e+01 pdb=" N9 A A1026 " -0.058 2.00e-02 2.50e+03 pdb=" C8 A A1026 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A A1026 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A1026 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A A1026 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A1026 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A A1026 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A A1026 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A A1026 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A A1026 " -0.003 2.00e-02 2.50e+03 ... (remaining 5266 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 9 1.79 - 2.57: 851 2.57 - 3.35: 74418 3.35 - 4.12: 206527 4.12 - 4.90: 311777 Nonbonded interactions: 593582 Sorted by model distance: nonbonded pdb=" N2 G A2099 " pdb=" O2 C A2471 " model vdw 1.016 2.496 nonbonded pdb=" N7 G A2096 " pdb=" O6 G A2098 " model vdw 1.382 3.120 nonbonded pdb=" O2' G A 251 " pdb=" OP1 A A2461 " model vdw 1.568 3.040 nonbonded pdb=" N6 A A2351 " pdb=" N6 A A2362 " model vdw 1.625 3.200 nonbonded pdb=" O6 G A2328 " pdb=" N2 G A2347 " model vdw 1.625 3.120 ... (remaining 593577 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.060 Extract box with map and model: 2.400 Check model and map are aligned: 0.410 Set scattering table: 0.510 Process input model: 177.510 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 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 : 0.011 0.129 75112 Z= 0.652 Angle : 0.963 20.794 113524 Z= 0.509 Chirality : 0.058 0.654 14668 Planarity : 0.006 0.149 5269 Dihedral : 24.717 179.593 44316 Min Nonbonded Distance : 1.016 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 15.23 % Favored : 84.33 % Rotamer: Outliers : 1.90 % Allowed : 12.66 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -5.38 (0.14), residues: 2048 helix: -3.90 (0.15), residues: 435 sheet: -3.29 (0.21), residues: 440 loop : -3.67 (0.14), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 65 HIS 0.012 0.002 HIS b 40 PHE 0.044 0.003 PHE Y 30 TYR 0.016 0.002 TYR C 83 ARG 0.016 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 2.692 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: L 55 MET cc_start: 0.3727 (ptm) cc_final: 0.3223 (ptt) outliers start: 33 outliers final: 19 residues processed: 322 average time/residue: 0.6861 time to fit residues: 370.0837 Evaluate side-chains 271 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 80 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 211 optimal weight: 40.0000 chunk 259 optimal weight: 8.9990 chunk 403 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS C 128 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS R 101 ASN S 37 ASN V 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 75112 Z= 0.218 Angle : 0.668 11.079 113524 Z= 0.344 Chirality : 0.039 0.327 14668 Planarity : 0.005 0.135 5269 Dihedral : 24.823 179.649 40149 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 91.99 % Rotamer: Outliers : 2.99 % Allowed : 15.54 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.18 (0.16), residues: 2048 helix: -2.65 (0.20), residues: 460 sheet: -2.58 (0.24), residues: 398 loop : -2.99 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 61 HIS 0.007 0.001 HIS U 44 PHE 0.013 0.002 PHE J 120 TYR 0.011 0.001 TYR R 2 ARG 0.006 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 2.785 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: V 70 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7157 (mtmt) REVERT: Z 3 LYS cc_start: 0.6200 (ptpp) cc_final: 0.5048 (ptpp) outliers start: 52 outliers final: 35 residues processed: 320 average time/residue: 0.6529 time to fit residues: 359.4722 Evaluate side-chains 293 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain Y residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 335 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 403 optimal weight: 10.0000 chunk 436 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 400 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 324 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN S 37 ASN V 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 75112 Z= 0.198 Angle : 0.603 9.624 113524 Z= 0.313 Chirality : 0.036 0.285 14668 Planarity : 0.005 0.126 5269 Dihedral : 24.704 177.244 40126 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.81 % Favored : 92.09 % Rotamer: Outliers : 3.11 % Allowed : 18.18 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.51 (0.17), residues: 2048 helix: -1.89 (0.23), residues: 464 sheet: -2.16 (0.25), residues: 384 loop : -2.66 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 61 HIS 0.005 0.001 HIS U 44 PHE 0.010 0.001 PHE Y 30 TYR 0.014 0.001 TYR R 2 ARG 0.005 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 34 residues processed: 320 average time/residue: 0.6701 time to fit residues: 367.6054 Evaluate side-chains 296 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain b residue 35 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.0670 chunk 303 optimal weight: 2.9990 chunk 209 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 chunk 192 optimal weight: 30.0000 chunk 271 optimal weight: 9.9990 chunk 405 optimal weight: 0.9990 chunk 429 optimal weight: 2.9990 chunk 211 optimal weight: 40.0000 chunk 384 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS V 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 75112 Z= 0.132 Angle : 0.557 9.682 113524 Z= 0.288 Chirality : 0.033 0.264 14668 Planarity : 0.004 0.119 5269 Dihedral : 24.585 177.507 40118 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.91 % Favored : 93.99 % Rotamer: Outliers : 3.16 % Allowed : 18.41 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.94 (0.17), residues: 2048 helix: -1.33 (0.24), residues: 462 sheet: -1.89 (0.25), residues: 408 loop : -2.29 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 61 HIS 0.003 0.001 HIS b 40 PHE 0.012 0.001 PHE Y 26 TYR 0.012 0.001 TYR T 69 ARG 0.005 0.000 ARG T 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 273 ARG cc_start: 0.3697 (mmt180) cc_final: 0.3473 (mmm160) REVERT: J 85 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6919 (pp) REVERT: V 70 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7331 (mttt) outliers start: 55 outliers final: 34 residues processed: 319 average time/residue: 0.6706 time to fit residues: 365.5980 Evaluate side-chains 302 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 37 HIS Chi-restraints excluded: chain Y residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 20.0000 chunk 243 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 177 optimal weight: 40.0000 chunk 366 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 70.0000 chunk 385 optimal weight: 8.9990 chunk 108 optimal weight: 60.0000 overall best weight: 12.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN V 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 75112 Z= 0.370 Angle : 0.686 14.803 113524 Z= 0.350 Chirality : 0.039 0.291 14668 Planarity : 0.005 0.119 5269 Dihedral : 24.668 177.373 40115 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 3.80 % Allowed : 18.76 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.91 (0.17), residues: 2048 helix: -1.05 (0.24), residues: 459 sheet: -2.00 (0.25), residues: 409 loop : -2.33 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 61 HIS 0.005 0.001 HIS b 40 PHE 0.024 0.002 PHE D 119 TYR 0.015 0.002 TYR L 74 ARG 0.008 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7153 (pp) outliers start: 66 outliers final: 51 residues processed: 306 average time/residue: 0.6598 time to fit residues: 345.9158 Evaluate side-chains 304 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 4 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 40.0000 chunk 386 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 105 optimal weight: 40.0000 chunk 429 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 198 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 75112 Z= 0.272 Angle : 0.629 13.211 113524 Z= 0.324 Chirality : 0.037 0.264 14668 Planarity : 0.005 0.117 5269 Dihedral : 24.639 177.082 40115 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.54 % Favored : 93.36 % Rotamer: Outliers : 3.74 % Allowed : 19.39 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.69 (0.17), residues: 2048 helix: -0.86 (0.25), residues: 461 sheet: -1.81 (0.26), residues: 390 loop : -2.22 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 61 HIS 0.005 0.001 HIS E 189 PHE 0.011 0.001 PHE R 40 TYR 0.030 0.001 TYR V 46 ARG 0.005 0.000 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7070 (pp) outliers start: 65 outliers final: 50 residues processed: 315 average time/residue: 0.6716 time to fit residues: 362.3991 Evaluate side-chains 312 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 4 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 313 optimal weight: 0.8980 chunk 243 optimal weight: 8.9990 chunk 361 optimal weight: 0.2980 chunk 239 optimal weight: 20.0000 chunk 427 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 197 optimal weight: 50.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 75112 Z= 0.172 Angle : 0.578 12.303 113524 Z= 0.298 Chirality : 0.034 0.254 14668 Planarity : 0.004 0.113 5269 Dihedral : 24.568 177.337 40115 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 3.11 % Allowed : 20.71 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.49 (0.18), residues: 2048 helix: -0.65 (0.25), residues: 454 sheet: -1.73 (0.25), residues: 408 loop : -2.09 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 61 HIS 0.004 0.001 HIS E 189 PHE 0.009 0.001 PHE Y 26 TYR 0.029 0.001 TYR V 46 ARG 0.005 0.000 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6920 (pp) outliers start: 54 outliers final: 48 residues processed: 303 average time/residue: 0.6640 time to fit residues: 346.3710 Evaluate side-chains 305 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 4 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 1.9990 chunk 170 optimal weight: 30.0000 chunk 255 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 211 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 75112 Z= 0.293 Angle : 0.633 11.035 113524 Z= 0.324 Chirality : 0.037 0.257 14668 Planarity : 0.005 0.114 5269 Dihedral : 24.580 176.715 40115 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.67 % Favored : 92.24 % Rotamer: Outliers : 3.86 % Allowed : 19.91 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.46 (0.18), residues: 2048 helix: -0.56 (0.25), residues: 449 sheet: -1.72 (0.25), residues: 400 loop : -2.08 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 61 HIS 0.005 0.001 HIS E 189 PHE 0.015 0.001 PHE D 119 TYR 0.017 0.001 TYR V 46 ARG 0.004 0.000 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7062 (pp) outliers start: 67 outliers final: 56 residues processed: 304 average time/residue: 0.6600 time to fit residues: 344.8914 Evaluate side-chains 310 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 4 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 8.9990 chunk 409 optimal weight: 0.8980 chunk 374 optimal weight: 9.9990 chunk 398 optimal weight: 0.2980 chunk 240 optimal weight: 20.0000 chunk 173 optimal weight: 30.0000 chunk 313 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 360 optimal weight: 20.0000 chunk 377 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 overall best weight: 5.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 75112 Z= 0.179 Angle : 0.585 11.495 113524 Z= 0.301 Chirality : 0.034 0.252 14668 Planarity : 0.004 0.111 5269 Dihedral : 24.542 177.538 40115 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.41 % Rotamer: Outliers : 2.88 % Allowed : 21.06 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.33 (0.18), residues: 2048 helix: -0.42 (0.25), residues: 446 sheet: -1.67 (0.25), residues: 409 loop : -1.99 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 61 HIS 0.004 0.001 HIS E 189 PHE 0.008 0.001 PHE Y 26 TYR 0.022 0.001 TYR V 46 ARG 0.004 0.000 ARG T 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 2.833 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: J 85 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6920 (pp) outliers start: 50 outliers final: 48 residues processed: 292 average time/residue: 0.6711 time to fit residues: 334.7721 Evaluate side-chains 306 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 30.0000 chunk 421 optimal weight: 30.0000 chunk 257 optimal weight: 6.9990 chunk 200 optimal weight: 50.0000 chunk 293 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 215 optimal weight: 30.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 75112 Z= 0.270 Angle : 0.625 10.791 113524 Z= 0.320 Chirality : 0.036 0.254 14668 Planarity : 0.005 0.112 5269 Dihedral : 24.542 176.930 40115 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.57 % Favored : 92.33 % Rotamer: Outliers : 3.05 % Allowed : 21.63 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.31 (0.18), residues: 2048 helix: -0.36 (0.25), residues: 450 sheet: -1.68 (0.25), residues: 400 loop : -2.00 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 61 HIS 0.005 0.001 HIS E 189 PHE 0.013 0.001 PHE D 119 TYR 0.015 0.001 TYR V 46 ARG 0.005 0.000 ARG T 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7053 (pp) outliers start: 53 outliers final: 49 residues processed: 294 average time/residue: 0.6644 time to fit residues: 335.6129 Evaluate side-chains 309 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 PHE Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain V residue 43 SER Chi-restraints excluded: chain V residue 53 ILE Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.0050 chunk 375 optimal weight: 6.9990 chunk 107 optimal weight: 60.0000 chunk 324 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 352 optimal weight: 0.1980 chunk 147 optimal weight: 20.0000 chunk 362 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 overall best weight: 7.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033865 restraints weight = 411134.854| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 1.70 r_work: 0.2606 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 75112 Z= 0.229 Angle : 0.611 10.856 113524 Z= 0.314 Chirality : 0.035 0.252 14668 Planarity : 0.004 0.112 5269 Dihedral : 24.538 177.003 40115 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.13 % Favored : 92.77 % Rotamer: Outliers : 2.99 % Allowed : 21.63 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.26 (0.18), residues: 2048 helix: -0.26 (0.25), residues: 449 sheet: -1.73 (0.25), residues: 408 loop : -1.95 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 61 HIS 0.005 0.001 HIS E 189 PHE 0.010 0.001 PHE V 80 TYR 0.021 0.001 TYR R 2 ARG 0.005 0.000 ARG T 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9630.99 seconds wall clock time: 172 minutes 51.67 seconds (10371.67 seconds total)