Starting phenix.real_space_refine on Fri Dec 27 23:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v2p_31659/12_2024/7v2p_31659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v2p_31659/12_2024/7v2p_31659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v2p_31659/12_2024/7v2p_31659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v2p_31659/12_2024/7v2p_31659.map" model { file = "/net/cci-nas-00/data/ceres_data/7v2p_31659/12_2024/7v2p_31659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v2p_31659/12_2024/7v2p_31659.cif" } resolution = 3.3 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1394 5.49 5 S 55 5.16 5 C 26691 2.51 5 N 9617 2.21 5 O 13376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51135 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 29962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1394, 29962 Classifications: {'RNA': 1394} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 93, 'rna3p_pur': 671, 'rna3p_pyr': 511} Link IDs: {'rna2p': 212, 'rna3p': 1181} Chain breaks: 2 Chain: "B" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1802 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 905 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 682 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Q" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 834 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "S" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "U" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2203 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33435 SG CYS D 9 91.165 73.511 88.459 1.00 54.05 S ATOM 33460 SG CYS D 12 92.486 76.306 91.260 1.00 54.64 S ATOM 33578 SG CYS D 26 94.344 72.276 89.586 1.00 58.25 S ATOM 33618 SG CYS D 31 95.481 74.957 88.319 1.00 60.42 S ATOM 44196 SG CYS N 24 65.934 120.027 47.764 1.00 46.61 S ATOM 44220 SG CYS N 27 64.413 118.658 50.822 1.00 45.75 S ATOM 44327 SG CYS N 40 65.197 122.542 50.610 1.00 43.89 S ATOM 44352 SG CYS N 43 68.029 120.267 50.855 1.00 44.15 S Time building chain proxies: 20.70, per 1000 atoms: 0.40 Number of scatterers: 51135 At special positions: 0 Unit cell: (143.52, 215.28, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 55 16.00 P 1394 15.00 O 13376 8.00 N 9617 7.00 C 26691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.80 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 12 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 23 sheets defined 44.0% alpha, 18.5% beta 481 base pairs and 726 stacking pairs defined. Time for finding SS restraints: 17.82 Creating SS restraints... Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.706A pdb=" N GLY B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.495A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 65 removed outlier: 3.663A pdb=" N THR B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.612A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 6.730A pdb=" N GLU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 129 " --> pdb=" O GLU B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 129' Processing helix chain 'B' and resid 131 through 150 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.533A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.899A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.594A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.733A pdb=" N TYR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.867A pdb=" N GLN D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 153 removed outlier: 3.637A pdb=" N ARG D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 150 through 153' Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.596A pdb=" N ALA D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 4.058A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.596A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 144 through 153 Processing helix chain 'F' and resid 15 through 33 removed outlier: 3.618A pdb=" N TYR F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 71 through 80 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.843A pdb=" N THR G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.818A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 removed outlier: 3.544A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.572A pdb=" N TYR G 151 " --> pdb=" O ASN G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.669A pdb=" N VAL H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 removed outlier: 3.566A pdb=" N GLU H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 40 through 46 removed outlier: 3.572A pdb=" N ALA I 43 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'J' and resid 13 through 30 Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 45 through 49 removed outlier: 3.792A pdb=" N GLY K 49 " --> pdb=" O GLY K 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 49' Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.679A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 75 Processing helix chain 'K' and resid 90 through 100 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.513A pdb=" N LEU M 48 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.571A pdb=" N TRP M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.665A pdb=" N LEU M 70 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.565A pdb=" N HIS O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.440A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 98 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 42 through 44 No H-bonds generated for 'chain 'R' and resid 42 through 44' Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 76 Processing helix chain 'S' and resid 12 through 24 removed outlier: 3.815A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.931A pdb=" N VAL S 45 " --> pdb=" O PRO S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 67 removed outlier: 3.573A pdb=" N MET S 66 " --> pdb=" O THR S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.540A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.848A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 93 removed outlier: 3.677A pdb=" N ARG T 89 " --> pdb=" O MET T 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 17 removed outlier: 4.072A pdb=" N LYS U 12 " --> pdb=" O PRO U 8 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 45 removed outlier: 3.576A pdb=" N ASN U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL U 41 " --> pdb=" O LEU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 68 removed outlier: 4.094A pdb=" N GLN U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 90 removed outlier: 4.127A pdb=" N LYS U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 115 removed outlier: 3.621A pdb=" N VAL U 111 " --> pdb=" O ASP U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 143 removed outlier: 3.978A pdb=" N THR U 134 " --> pdb=" O TYR U 130 " (cutoff:3.500A) Proline residue: U 135 - end of helix Processing helix chain 'U' and resid 155 through 164 removed outlier: 3.524A pdb=" N ALA U 159 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG U 161 " --> pdb=" O GLU U 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'U' and resid 220 through 232 removed outlier: 3.522A pdb=" N PHE U 232 " --> pdb=" O ILE U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 247 Processing helix chain 'U' and resid 253 through 264 removed outlier: 3.619A pdb=" N GLU U 262 " --> pdb=" O GLU U 258 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 275 Processing helix chain 'U' and resid 276 through 288 Processing helix chain 'V' and resid 8 through 16 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.942A pdb=" N PHE B 17 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 42 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS B 19 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.132A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 69 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE B 162 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 184 " --> pdb=" O TYR B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.582A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.945A pdb=" N ASP D 144 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 6.746A pdb=" N LEU E 31 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE E 13 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY E 29 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG E 15 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG E 27 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA E 17 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG E 25 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET E 19 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY E 23 " --> pdb=" O MET E 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 52 removed outlier: 6.927A pdb=" N GLU F 38 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N GLU F 66 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL F 40 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN F 64 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU F 42 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TRP F 62 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 58 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.981A pdb=" N ALA F 99 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE R 29 " --> pdb=" O ALA F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 73 through 80 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 85 removed outlier: 3.719A pdb=" N GLU H 136 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 83 through 85 removed outlier: 3.719A pdb=" N GLU H 136 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE H 111 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU H 136 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 109 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'J' and resid 38 through 49 removed outlier: 6.920A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 38 through 49 removed outlier: 6.920A pdb=" N LEU J 71 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 39 through 44 removed outlier: 5.947A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.594A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.579A pdb=" N ILE P 19 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR P 17 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.743A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Q 9 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC5, first strand: chain 'U' and resid 96 through 99 removed outlier: 6.706A pdb=" N VAL U 73 " --> pdb=" O THR U 97 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE U 99 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA U 75 " --> pdb=" O ILE U 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE U 53 " --> pdb=" O MET U 123 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE U 122 " --> pdb=" O GLY U 149 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N VAL U 151 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL U 124 " --> pdb=" O VAL U 151 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N MET U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA U 126 " --> pdb=" O MET U 153 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER U 203 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG U 207 " --> pdb=" O THR U 186 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR U 186 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE U 209 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA U 184 " --> pdb=" O ILE U 209 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1268 hydrogen bonds 2058 hydrogen bond angles 0 basepair planarities 481 basepair parallelities 726 stacking parallelities Total time for adding SS restraints: 37.16 Time building geometry restraints manager: 10.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6482 1.33 - 1.45: 23223 1.45 - 1.58: 22456 1.58 - 1.70: 2785 1.70 - 1.82: 96 Bond restraints: 55042 Sorted by residual: bond pdb=" C GLN U 198 " pdb=" N PRO U 199 " ideal model delta sigma weight residual 1.331 1.355 -0.024 7.90e-03 1.60e+04 9.20e+00 bond pdb=" C LEU U 247 " pdb=" N PRO U 248 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.27e-02 6.20e+03 6.90e+00 bond pdb=" C SER B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.89e+00 bond pdb=" C VAL U 196 " pdb=" N PRO U 197 " ideal model delta sigma weight residual 1.335 1.358 -0.023 8.70e-03 1.32e+04 6.83e+00 bond pdb=" C ARG D 36 " pdb=" N PRO D 37 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.25e+00 ... (remaining 55037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 73962 1.92 - 3.84: 6465 3.84 - 5.76: 758 5.76 - 7.67: 17 7.67 - 9.59: 9 Bond angle restraints: 81211 Sorted by residual: angle pdb=" O3' U A 970 " pdb=" C3' U A 970 " pdb=" C2' U A 970 " ideal model delta sigma weight residual 109.50 119.09 -9.59 1.50e+00 4.44e-01 4.09e+01 angle pdb=" C4' U A 862 " pdb=" C3' U A 862 " pdb=" O3' U A 862 " ideal model delta sigma weight residual 109.40 118.92 -9.52 1.50e+00 4.44e-01 4.03e+01 angle pdb=" C4' G A1036 " pdb=" C3' G A1036 " pdb=" O3' G A1036 " ideal model delta sigma weight residual 109.40 118.86 -9.46 1.50e+00 4.44e-01 3.98e+01 angle pdb=" O3' G A1036 " pdb=" C3' G A1036 " pdb=" C2' G A1036 " ideal model delta sigma weight residual 109.50 118.94 -9.44 1.50e+00 4.44e-01 3.96e+01 angle pdb=" C4' A A 979 " pdb=" C3' A A 979 " pdb=" O3' A A 979 " ideal model delta sigma weight residual 109.40 118.47 -9.07 1.50e+00 4.44e-01 3.66e+01 ... (remaining 81206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 31677 35.72 - 71.45: 3362 71.45 - 107.17: 479 107.17 - 142.89: 7 142.89 - 178.62: 14 Dihedral angle restraints: 35539 sinusoidal: 27950 harmonic: 7589 Sorted by residual: dihedral pdb=" C5' U A1118 " pdb=" C4' U A1118 " pdb=" C3' U A1118 " pdb=" O3' U A1118 " ideal model delta sinusoidal sigma weight residual 147.00 82.96 64.04 1 8.00e+00 1.56e-02 8.43e+01 dihedral pdb=" O4' U A 361 " pdb=" C1' U A 361 " pdb=" N1 U A 361 " pdb=" C2 U A 361 " ideal model delta sinusoidal sigma weight residual 200.00 51.47 148.53 1 1.50e+01 4.44e-03 7.91e+01 dihedral pdb=" C4' U A1118 " pdb=" C3' U A1118 " pdb=" C2' U A1118 " pdb=" C1' U A1118 " ideal model delta sinusoidal sigma weight residual -35.00 25.46 -60.46 1 8.00e+00 1.56e-02 7.60e+01 ... (remaining 35536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 8910 0.150 - 0.301: 1228 0.301 - 0.451: 8 0.451 - 0.601: 2 0.601 - 0.752: 3 Chirality restraints: 10151 Sorted by residual: chirality pdb=" C3' G A1036 " pdb=" C4' G A1036 " pdb=" O3' G A1036 " pdb=" C2' G A1036 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C3' A A 979 " pdb=" C4' A A 979 " pdb=" O3' A A 979 " pdb=" C2' A A 979 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.36e+00 chirality pdb=" C3' U A 970 " pdb=" C4' U A 970 " pdb=" O3' U A 970 " pdb=" C2' U A 970 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.04e+00 ... (remaining 10148 not shown) Planarity restraints: 5125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 577 " 0.004 2.00e-02 2.50e+03 1.83e-02 1.00e+01 pdb=" N9 G A 577 " -0.000 2.00e-02 2.50e+03 pdb=" C8 G A 577 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A 577 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A 577 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 577 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G A 577 " 0.023 2.00e-02 2.50e+03 pdb=" N1 G A 577 " -0.045 2.00e-02 2.50e+03 pdb=" C2 G A 577 " 0.035 2.00e-02 2.50e+03 pdb=" N2 G A 577 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 577 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 577 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1503 " -0.004 2.00e-02 2.50e+03 1.74e-02 9.13e+00 pdb=" N9 G A1503 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G A1503 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G A1503 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G A1503 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A1503 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G A1503 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G A1503 " -0.042 2.00e-02 2.50e+03 pdb=" C2 G A1503 " 0.038 2.00e-02 2.50e+03 pdb=" N2 G A1503 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G A1503 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A1503 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 23 " -0.000 2.00e-02 2.50e+03 1.54e-02 7.08e+00 pdb=" N9 G A 23 " -0.001 2.00e-02 2.50e+03 pdb=" C8 G A 23 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 23 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 23 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 23 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G A 23 " 0.025 2.00e-02 2.50e+03 pdb=" N1 G A 23 " -0.034 2.00e-02 2.50e+03 pdb=" C2 G A 23 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G A 23 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 23 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G A 23 " 0.003 2.00e-02 2.50e+03 ... (remaining 5122 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6823 2.76 - 3.30: 44937 3.30 - 3.83: 102271 3.83 - 4.37: 124222 4.37 - 4.90: 174355 Nonbonded interactions: 452608 Sorted by model distance: nonbonded pdb=" O SER Q 66 " pdb=" NH1 ARG Q 70 " model vdw 2.228 3.120 nonbonded pdb=" O6 G A 78 " pdb=" O4 U A 86 " model vdw 2.237 2.432 nonbonded pdb=" N3 A A 352 " pdb=" O2' U A 364 " model vdw 2.241 3.120 nonbonded pdb=" O ILE U 85 " pdb=" OG1 THR U 89 " model vdw 2.249 3.040 nonbonded pdb=" O VAL U 103 " pdb=" NZ LYS U 139 " model vdw 2.251 3.120 ... (remaining 452603 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.550 Check model and map are aligned: 0.280 Set scattering table: 0.370 Process input model: 117.890 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 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 : 0.008 0.043 55042 Z= 0.477 Angle : 1.093 9.592 81211 Z= 0.691 Chirality : 0.100 0.752 10151 Planarity : 0.004 0.018 5125 Dihedral : 23.039 178.616 30655 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.40 % Favored : 93.37 % Rotamer: Outliers : 0.27 % Allowed : 4.19 % Favored : 95.54 % Cbeta Deviations : 0.12 % 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: -0.50 (0.16), residues: 2595 helix: 0.65 (0.16), residues: 1041 sheet: 0.16 (0.26), residues: 420 loop : -1.45 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 138 HIS 0.007 0.002 HIS P 13 PHE 0.015 0.002 PHE D 79 TYR 0.016 0.002 TYR L 117 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 397 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7985 (tp-100) REVERT: C 139 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7404 (tp-100) REVERT: D 134 ASP cc_start: 0.8509 (p0) cc_final: 0.8265 (p0) REVERT: E 19 MET cc_start: 0.8255 (mmm) cc_final: 0.7888 (mmt) REVERT: E 72 GLN cc_start: 0.8535 (pm20) cc_final: 0.8099 (pm20) REVERT: F 92 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8505 (ttmm) REVERT: G 12 LEU cc_start: 0.8967 (mt) cc_final: 0.8744 (mt) REVERT: I 60 ASP cc_start: 0.7205 (m-30) cc_final: 0.6196 (p0) REVERT: K 54 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7946 (mtt180) REVERT: K 108 ILE cc_start: 0.9245 (mt) cc_final: 0.8902 (mt) REVERT: M 31 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8451 (ttpp) REVERT: M 35 GLU cc_start: 0.7939 (pt0) cc_final: 0.7577 (pt0) REVERT: O 59 MET cc_start: 0.9054 (mtt) cc_final: 0.8738 (mtt) REVERT: P 50 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8429 (ttmm) REVERT: S 18 LYS cc_start: 0.6963 (mttt) cc_final: 0.6737 (mttt) REVERT: T 37 SER cc_start: 0.8653 (t) cc_final: 0.8363 (t) REVERT: V 10 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7790 (ttm-80) outliers start: 6 outliers final: 1 residues processed: 401 average time/residue: 0.5287 time to fit residues: 345.6215 Evaluate side-chains 342 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 chunk 165 optimal weight: 0.0570 chunk 101 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 136 GLN C 162 GLN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN S 47 HIS T 75 ASN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55042 Z= 0.194 Angle : 0.556 8.444 81211 Z= 0.293 Chirality : 0.036 0.319 10151 Planarity : 0.004 0.045 5125 Dihedral : 23.584 179.888 25172 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.82 % Favored : 95.03 % Rotamer: Outliers : 0.90 % Allowed : 9.74 % Favored : 89.36 % 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: 0.01 (0.17), residues: 2595 helix: 1.13 (0.16), residues: 1077 sheet: 0.01 (0.26), residues: 454 loop : -1.14 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.005 0.001 HIS L 77 PHE 0.015 0.001 PHE G 62 TYR 0.013 0.001 TYR P 32 ARG 0.004 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 351 time to evaluate : 2.654 Fit side-chains revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8471 (p0) cc_final: 0.8059 (p0) REVERT: B 113 HIS cc_start: 0.7224 (m170) cc_final: 0.6956 (m170) REVERT: B 212 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7861 (tp-100) REVERT: C 17 ASP cc_start: 0.7430 (t0) cc_final: 0.7089 (t0) REVERT: C 139 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7328 (tp-100) REVERT: D 144 ASP cc_start: 0.8248 (m-30) cc_final: 0.7688 (t0) REVERT: E 19 MET cc_start: 0.8304 (mmm) cc_final: 0.7928 (mmt) REVERT: E 41 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8781 (p) REVERT: E 72 GLN cc_start: 0.8521 (pm20) cc_final: 0.8096 (pm20) REVERT: F 1 MET cc_start: 0.7755 (tpt) cc_final: 0.7414 (tpp) REVERT: I 60 ASP cc_start: 0.7053 (m-30) cc_final: 0.5928 (p0) REVERT: K 108 ILE cc_start: 0.9212 (mt) cc_final: 0.8862 (mt) REVERT: K 111 ASP cc_start: 0.8780 (t70) cc_final: 0.8526 (t70) REVERT: M 35 GLU cc_start: 0.7985 (pt0) cc_final: 0.7688 (pt0) REVERT: M 65 LYS cc_start: 0.6639 (tppt) cc_final: 0.6354 (tppt) REVERT: O 59 MET cc_start: 0.9123 (mtt) cc_final: 0.8880 (mtt) REVERT: P 50 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8399 (ttmm) REVERT: P 52 ASP cc_start: 0.8540 (t70) cc_final: 0.8326 (t70) REVERT: R 41 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8521 (mtpp) REVERT: T 85 MET cc_start: 0.8313 (mtp) cc_final: 0.7896 (mtm) REVERT: V 10 ARG cc_start: 0.8393 (tpp80) cc_final: 0.7997 (ttm-80) outliers start: 20 outliers final: 15 residues processed: 360 average time/residue: 0.5131 time to fit residues: 305.8125 Evaluate side-chains 350 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 334 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 249 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 386 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 136 GLN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 55042 Z= 0.267 Angle : 0.582 8.627 81211 Z= 0.303 Chirality : 0.037 0.388 10151 Planarity : 0.004 0.048 5125 Dihedral : 23.492 179.013 25172 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 1.67 % Allowed : 11.81 % Favored : 86.52 % 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: 0.00 (0.17), residues: 2595 helix: 1.13 (0.16), residues: 1077 sheet: 0.01 (0.26), residues: 449 loop : -1.15 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 24 HIS 0.007 0.001 HIS U 43 PHE 0.014 0.002 PHE H 31 TYR 0.015 0.002 TYR P 32 ARG 0.004 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 2.717 Fit side-chains revert: symmetry clash REVERT: B 37 ASN cc_start: 0.8480 (p0) cc_final: 0.8048 (p0) REVERT: B 113 HIS cc_start: 0.7135 (m170) cc_final: 0.6871 (m170) REVERT: B 212 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7788 (tp-100) REVERT: C 139 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7338 (tp-100) REVERT: D 144 ASP cc_start: 0.8294 (m-30) cc_final: 0.7711 (t0) REVERT: E 19 MET cc_start: 0.8313 (mmm) cc_final: 0.7921 (mmm) REVERT: E 41 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8768 (p) REVERT: E 72 GLN cc_start: 0.8484 (pm20) cc_final: 0.8129 (pm20) REVERT: G 86 GLN cc_start: 0.8692 (mp10) cc_final: 0.8418 (mm-40) REVERT: I 60 ASP cc_start: 0.7177 (m-30) cc_final: 0.5971 (p0) REVERT: J 99 LYS cc_start: 0.7620 (tptp) cc_final: 0.7287 (tptp) REVERT: K 108 ILE cc_start: 0.9197 (mt) cc_final: 0.8828 (mt) REVERT: K 111 ASP cc_start: 0.8829 (t70) cc_final: 0.8557 (t70) REVERT: M 35 GLU cc_start: 0.8030 (pt0) cc_final: 0.7785 (pt0) REVERT: P 50 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8372 (ttmm) REVERT: R 36 ASN cc_start: 0.8538 (t0) cc_final: 0.7527 (t0) REVERT: R 38 GLU cc_start: 0.8379 (pm20) cc_final: 0.8116 (pm20) REVERT: R 41 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8507 (mtpp) REVERT: T 46 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7331 (mm-30) REVERT: T 85 MET cc_start: 0.8469 (mtp) cc_final: 0.8121 (mtm) outliers start: 37 outliers final: 28 residues processed: 362 average time/residue: 0.5209 time to fit residues: 312.0601 Evaluate side-chains 359 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 249 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN F 27 GLN G 84 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 55042 Z= 0.413 Angle : 0.672 9.726 81211 Z= 0.345 Chirality : 0.042 0.356 10151 Planarity : 0.005 0.053 5125 Dihedral : 23.509 178.351 25172 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.51 % Favored : 93.37 % Rotamer: Outliers : 2.48 % Allowed : 13.57 % Favored : 83.95 % 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: -0.26 (0.17), residues: 2595 helix: 0.88 (0.16), residues: 1072 sheet: -0.11 (0.26), residues: 445 loop : -1.24 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 138 HIS 0.009 0.002 HIS N 49 PHE 0.015 0.002 PHE U 195 TYR 0.018 0.002 TYR P 32 ARG 0.007 0.001 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 2.734 Fit side-chains REVERT: B 37 ASN cc_start: 0.8467 (p0) cc_final: 0.8041 (p0) REVERT: B 135 GLN cc_start: 0.8119 (mt0) cc_final: 0.7803 (mt0) REVERT: B 212 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7813 (tp-100) REVERT: C 139 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7317 (tp-100) REVERT: E 19 MET cc_start: 0.8431 (mmm) cc_final: 0.8131 (mmm) REVERT: E 72 GLN cc_start: 0.8478 (pm20) cc_final: 0.8071 (pm20) REVERT: G 20 ASP cc_start: 0.7167 (p0) cc_final: 0.6736 (p0) REVERT: I 60 ASP cc_start: 0.7175 (m-30) cc_final: 0.5880 (p0) REVERT: K 108 ILE cc_start: 0.9259 (mt) cc_final: 0.8942 (mt) REVERT: K 111 ASP cc_start: 0.8768 (t70) cc_final: 0.8511 (t70) REVERT: O 84 LYS cc_start: 0.8605 (tttp) cc_final: 0.8386 (tttm) REVERT: P 50 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8402 (ttmm) REVERT: R 41 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8523 (mtpp) REVERT: T 85 MET cc_start: 0.8496 (mtp) cc_final: 0.8161 (mtm) outliers start: 55 outliers final: 42 residues processed: 383 average time/residue: 0.5146 time to fit residues: 327.0082 Evaluate side-chains 376 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 324 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 340 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS C 98 ASN F 27 GLN G 84 ASN J 13 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55042 Z= 0.168 Angle : 0.543 10.433 81211 Z= 0.284 Chirality : 0.035 0.319 10151 Planarity : 0.004 0.049 5125 Dihedral : 23.450 179.166 25169 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.01 % Favored : 94.84 % Rotamer: Outliers : 1.62 % Allowed : 15.15 % Favored : 83.23 % 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: 0.14 (0.17), residues: 2595 helix: 1.26 (0.16), residues: 1071 sheet: 0.10 (0.26), residues: 432 loop : -1.07 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 138 HIS 0.006 0.001 HIS B 113 PHE 0.012 0.001 PHE G 62 TYR 0.013 0.001 TYR C 48 ARG 0.009 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 2.682 Fit side-chains REVERT: B 135 GLN cc_start: 0.8034 (mt0) cc_final: 0.7630 (mt0) REVERT: B 212 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7681 (tp-100) REVERT: C 139 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7309 (tp-100) REVERT: E 41 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8769 (p) REVERT: E 72 GLN cc_start: 0.8417 (pm20) cc_final: 0.8029 (pm20) REVERT: F 1 MET cc_start: 0.7093 (tpp) cc_final: 0.6862 (mmm) REVERT: G 16 LEU cc_start: 0.8664 (mp) cc_final: 0.8330 (mp) REVERT: G 20 ASP cc_start: 0.7195 (p0) cc_final: 0.6775 (p0) REVERT: G 86 GLN cc_start: 0.8634 (mp10) cc_final: 0.8339 (mm-40) REVERT: I 60 ASP cc_start: 0.7051 (m-30) cc_final: 0.5983 (p0) REVERT: J 86 MET cc_start: 0.7587 (mpp) cc_final: 0.7353 (mpp) REVERT: K 108 ILE cc_start: 0.9256 (mt) cc_final: 0.8988 (mt) REVERT: K 111 ASP cc_start: 0.8764 (t70) cc_final: 0.8489 (t70) REVERT: M 31 LYS cc_start: 0.8641 (tttm) cc_final: 0.8297 (ptmt) REVERT: M 34 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7747 (tt) REVERT: O 84 LYS cc_start: 0.8644 (tttp) cc_final: 0.8423 (tttm) REVERT: P 50 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8356 (ttmm) REVERT: R 41 LYS cc_start: 0.8813 (mtpp) cc_final: 0.8410 (mtpp) REVERT: S 44 MET cc_start: 0.8195 (mtp) cc_final: 0.7705 (mtm) REVERT: T 46 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7468 (mm-30) REVERT: T 85 MET cc_start: 0.8470 (mtp) cc_final: 0.8150 (mtm) REVERT: T 92 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8069 (mm) outliers start: 36 outliers final: 22 residues processed: 374 average time/residue: 0.5172 time to fit residues: 320.7192 Evaluate side-chains 360 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 335 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 128 LEU Chi-restraints excluded: chain U residue 134 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 199 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 98 ASN C 136 GLN G 84 ASN K 13 GLN O 37 ASN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.143 55042 Z= 0.670 Angle : 0.838 10.358 81211 Z= 0.419 Chirality : 0.050 0.370 10151 Planarity : 0.007 0.080 5125 Dihedral : 23.547 179.848 25169 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 3.43 % Allowed : 14.88 % Favored : 81.70 % 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: -0.57 (0.16), residues: 2595 helix: 0.61 (0.16), residues: 1062 sheet: -0.27 (0.25), residues: 439 loop : -1.38 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 138 HIS 0.012 0.002 HIS N 49 PHE 0.021 0.003 PHE C 203 TYR 0.025 0.003 TYR L 117 ARG 0.010 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 335 time to evaluate : 2.669 Fit side-chains REVERT: B 135 GLN cc_start: 0.8049 (mt0) cc_final: 0.7757 (mt0) REVERT: B 212 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7738 (tp-100) REVERT: C 178 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9016 (mm) REVERT: E 19 MET cc_start: 0.8438 (mmm) cc_final: 0.8044 (mtp) REVERT: E 72 GLN cc_start: 0.8461 (pm20) cc_final: 0.8120 (pm20) REVERT: F 1 MET cc_start: 0.7180 (tpp) cc_final: 0.6958 (mmm) REVERT: F 39 LYS cc_start: 0.8520 (ptmt) cc_final: 0.8309 (ptmm) REVERT: G 16 LEU cc_start: 0.8692 (mp) cc_final: 0.8383 (mp) REVERT: G 20 ASP cc_start: 0.7234 (p0) cc_final: 0.6849 (p0) REVERT: I 48 GLU cc_start: 0.8111 (mp0) cc_final: 0.7834 (mp0) REVERT: I 60 ASP cc_start: 0.7182 (m-30) cc_final: 0.5901 (p0) REVERT: J 25 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7775 (tp30) REVERT: J 73 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: J 86 MET cc_start: 0.7608 (mpp) cc_final: 0.7363 (mpp) REVERT: K 108 ILE cc_start: 0.9266 (mt) cc_final: 0.8962 (mt) REVERT: K 111 ASP cc_start: 0.8794 (t70) cc_final: 0.8573 (t70) REVERT: O 84 LYS cc_start: 0.8743 (tttp) cc_final: 0.8522 (tttm) REVERT: P 50 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8425 (ttmm) REVERT: R 41 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8536 (mtpp) REVERT: S 40 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7684 (mp) REVERT: T 85 MET cc_start: 0.8535 (mtp) cc_final: 0.8198 (mtm) outliers start: 76 outliers final: 60 residues processed: 384 average time/residue: 0.5227 time to fit residues: 337.0181 Evaluate side-chains 390 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 327 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 55 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 128 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN F 27 GLN J 84 GLN K 117 ASN U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55042 Z= 0.181 Angle : 0.567 10.861 81211 Z= 0.296 Chirality : 0.036 0.295 10151 Planarity : 0.004 0.049 5125 Dihedral : 23.449 178.760 25169 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 2.52 % Allowed : 16.19 % Favored : 81.29 % 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: -0.08 (0.17), residues: 2595 helix: 1.08 (0.16), residues: 1070 sheet: -0.07 (0.26), residues: 432 loop : -1.16 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 138 HIS 0.003 0.001 HIS N 49 PHE 0.013 0.001 PHE G 62 TYR 0.016 0.001 TYR G 85 ARG 0.007 0.000 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 2.650 Fit side-chains REVERT: B 33 TYR cc_start: 0.8662 (t80) cc_final: 0.8368 (t80) REVERT: B 135 GLN cc_start: 0.8044 (mt0) cc_final: 0.7703 (mt0) REVERT: B 212 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7679 (tp-100) REVERT: C 139 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7754 (tp-100) REVERT: D 144 ASP cc_start: 0.8366 (m-30) cc_final: 0.7715 (t0) REVERT: E 41 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8748 (p) REVERT: E 72 GLN cc_start: 0.8336 (pm20) cc_final: 0.7938 (pm20) REVERT: F 1 MET cc_start: 0.7062 (tpp) cc_final: 0.6788 (mmm) REVERT: G 16 LEU cc_start: 0.8660 (mp) cc_final: 0.8348 (mp) REVERT: G 20 ASP cc_start: 0.7150 (p0) cc_final: 0.6733 (p0) REVERT: G 86 GLN cc_start: 0.8615 (mp10) cc_final: 0.8358 (mm-40) REVERT: G 154 TYR cc_start: 0.7531 (m-80) cc_final: 0.7316 (m-10) REVERT: I 60 ASP cc_start: 0.7005 (m-30) cc_final: 0.5890 (p0) REVERT: J 73 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: J 86 MET cc_start: 0.7606 (mpp) cc_final: 0.7356 (mpp) REVERT: K 108 ILE cc_start: 0.9259 (mt) cc_final: 0.9000 (mt) REVERT: K 111 ASP cc_start: 0.8772 (t70) cc_final: 0.8527 (t70) REVERT: M 31 LYS cc_start: 0.8706 (tttm) cc_final: 0.8416 (ptmt) REVERT: M 34 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7612 (tt) REVERT: P 50 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8349 (ttmm) REVERT: R 41 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8413 (mtpp) REVERT: T 85 MET cc_start: 0.8461 (mtp) cc_final: 0.8152 (mtm) REVERT: T 92 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8058 (mm) outliers start: 56 outliers final: 36 residues processed: 379 average time/residue: 0.5180 time to fit residues: 325.9779 Evaluate side-chains 377 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain U residue 264 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 297 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN T 42 GLN U 43 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 55042 Z= 0.138 Angle : 0.530 11.265 81211 Z= 0.277 Chirality : 0.034 0.242 10151 Planarity : 0.004 0.050 5125 Dihedral : 23.416 178.749 25169 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 1.85 % Allowed : 16.95 % Favored : 81.20 % 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: 0.21 (0.17), residues: 2595 helix: 1.38 (0.16), residues: 1071 sheet: 0.11 (0.26), residues: 427 loop : -1.08 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 138 HIS 0.004 0.001 HIS U 144 PHE 0.012 0.001 PHE G 62 TYR 0.017 0.001 TYR C 48 ARG 0.008 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 2.651 Fit side-chains revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8755 (t80) cc_final: 0.8484 (t80) REVERT: B 135 GLN cc_start: 0.7992 (mt0) cc_final: 0.7540 (mt0) REVERT: B 212 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7630 (tp-100) REVERT: C 139 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7199 (tp-100) REVERT: D 27 TYR cc_start: 0.8219 (m-80) cc_final: 0.7801 (m-80) REVERT: D 144 ASP cc_start: 0.8305 (m-30) cc_final: 0.7680 (t0) REVERT: E 41 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8761 (p) REVERT: E 72 GLN cc_start: 0.8361 (pm20) cc_final: 0.8095 (pm20) REVERT: F 1 MET cc_start: 0.7017 (tpp) cc_final: 0.6630 (mmm) REVERT: F 47 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7664 (ttm-80) REVERT: F 63 TYR cc_start: 0.8430 (m-80) cc_final: 0.8165 (m-10) REVERT: G 16 LEU cc_start: 0.8602 (mp) cc_final: 0.8309 (mp) REVERT: G 20 ASP cc_start: 0.7158 (p0) cc_final: 0.6771 (p0) REVERT: G 86 GLN cc_start: 0.8636 (mp10) cc_final: 0.8356 (mm-40) REVERT: G 154 TYR cc_start: 0.7429 (m-80) cc_final: 0.7014 (m-10) REVERT: I 60 ASP cc_start: 0.7145 (m-30) cc_final: 0.5966 (p0) REVERT: J 84 GLN cc_start: 0.7166 (pt0) cc_final: 0.6541 (pm20) REVERT: J 86 MET cc_start: 0.7610 (mpp) cc_final: 0.7343 (mpp) REVERT: K 108 ILE cc_start: 0.9265 (mt) cc_final: 0.8995 (mt) REVERT: K 111 ASP cc_start: 0.8732 (t70) cc_final: 0.8492 (t70) REVERT: L 44 LYS cc_start: 0.7756 (tptp) cc_final: 0.7343 (tppt) REVERT: M 31 LYS cc_start: 0.8704 (tttm) cc_final: 0.8417 (ptmt) REVERT: M 34 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7701 (tt) REVERT: P 50 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8327 (ttmm) REVERT: R 36 ASN cc_start: 0.8567 (t0) cc_final: 0.8220 (t0) REVERT: R 41 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8446 (mtpp) REVERT: S 44 MET cc_start: 0.8455 (mtp) cc_final: 0.8027 (mtm) REVERT: T 42 GLN cc_start: 0.8411 (tm130) cc_final: 0.8166 (tm-30) REVERT: T 46 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6749 (mm-30) REVERT: T 48 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7835 (mppt) REVERT: T 85 MET cc_start: 0.8414 (mtp) cc_final: 0.8066 (mtm) outliers start: 41 outliers final: 29 residues processed: 383 average time/residue: 0.5188 time to fit residues: 327.6995 Evaluate side-chains 373 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 341 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 48 LYS Chi-restraints excluded: chain U residue 128 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 5.9990 chunk 362 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 333 optimal weight: 0.0980 chunk 351 optimal weight: 0.0270 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 108 ASN F 27 GLN G 84 ASN S 47 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55042 Z= 0.169 Angle : 0.530 10.795 81211 Z= 0.275 Chirality : 0.034 0.233 10151 Planarity : 0.004 0.048 5125 Dihedral : 23.372 177.856 25169 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 1.85 % Allowed : 17.27 % Favored : 80.88 % 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: 0.25 (0.17), residues: 2595 helix: 1.42 (0.16), residues: 1073 sheet: 0.02 (0.26), residues: 438 loop : -1.04 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 138 HIS 0.003 0.001 HIS U 144 PHE 0.014 0.001 PHE G 62 TYR 0.013 0.001 TYR I 4 ARG 0.008 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 343 time to evaluate : 2.660 Fit side-chains revert: symmetry clash REVERT: B 8 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6929 (pttm) REVERT: B 33 TYR cc_start: 0.8760 (t80) cc_final: 0.8506 (t80) REVERT: B 135 GLN cc_start: 0.7983 (mt0) cc_final: 0.7549 (mt0) REVERT: B 212 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7637 (tp-100) REVERT: C 139 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7196 (tp-100) REVERT: D 27 TYR cc_start: 0.8209 (m-80) cc_final: 0.7786 (m-80) REVERT: D 144 ASP cc_start: 0.8333 (m-30) cc_final: 0.7708 (t0) REVERT: E 41 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8756 (p) REVERT: E 72 GLN cc_start: 0.8354 (pm20) cc_final: 0.8072 (pm20) REVERT: F 1 MET cc_start: 0.7068 (tpp) cc_final: 0.6665 (mmm) REVERT: F 63 TYR cc_start: 0.8434 (m-80) cc_final: 0.8164 (m-10) REVERT: G 16 LEU cc_start: 0.8596 (mp) cc_final: 0.8283 (mp) REVERT: G 86 GLN cc_start: 0.8656 (mp10) cc_final: 0.8358 (mm-40) REVERT: G 154 TYR cc_start: 0.7413 (m-80) cc_final: 0.7057 (m-10) REVERT: I 60 ASP cc_start: 0.7013 (m-30) cc_final: 0.5901 (p0) REVERT: J 86 MET cc_start: 0.7598 (mpp) cc_final: 0.7330 (mpp) REVERT: K 108 ILE cc_start: 0.9266 (mt) cc_final: 0.8986 (mt) REVERT: K 111 ASP cc_start: 0.8752 (t70) cc_final: 0.8504 (t70) REVERT: M 31 LYS cc_start: 0.8684 (tttm) cc_final: 0.8405 (ptmt) REVERT: M 34 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7689 (tt) REVERT: M 65 LYS cc_start: 0.6595 (tppt) cc_final: 0.6310 (tppt) REVERT: P 50 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8350 (ttmm) REVERT: R 36 ASN cc_start: 0.8528 (t0) cc_final: 0.8226 (t0) REVERT: R 41 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8439 (mtpp) REVERT: S 44 MET cc_start: 0.8462 (mtp) cc_final: 0.8050 (mtm) REVERT: T 46 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6855 (mm-30) REVERT: T 85 MET cc_start: 0.8500 (mtp) cc_final: 0.8236 (mtm) outliers start: 41 outliers final: 31 residues processed: 367 average time/residue: 0.5238 time to fit residues: 317.3153 Evaluate side-chains 371 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 0.7980 chunk 373 optimal weight: 4.9990 chunk 227 optimal weight: 0.0370 chunk 177 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 391 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 0.0370 chunk 191 optimal weight: 0.8980 overall best weight: 1.1538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN S 47 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 55042 Z= 0.144 Angle : 0.532 10.461 81211 Z= 0.275 Chirality : 0.033 0.229 10151 Planarity : 0.004 0.064 5125 Dihedral : 23.382 177.883 25169 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.01 % Favored : 94.87 % Rotamer: Outliers : 1.71 % Allowed : 17.36 % Favored : 80.93 % 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: 0.29 (0.17), residues: 2595 helix: 1.44 (0.16), residues: 1073 sheet: 0.09 (0.26), residues: 433 loop : -1.02 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 167 HIS 0.004 0.001 HIS U 144 PHE 0.014 0.001 PHE G 62 TYR 0.015 0.001 TYR M 59 ARG 0.009 0.000 ARG D 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 33 TYR cc_start: 0.8755 (t80) cc_final: 0.8509 (t80) REVERT: B 135 GLN cc_start: 0.7981 (mt0) cc_final: 0.7550 (mt0) REVERT: B 212 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7628 (tp-100) REVERT: C 139 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7212 (tp-100) REVERT: D 27 TYR cc_start: 0.8180 (m-80) cc_final: 0.7751 (m-80) REVERT: D 144 ASP cc_start: 0.8323 (m-30) cc_final: 0.7698 (t0) REVERT: E 41 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8760 (p) REVERT: E 72 GLN cc_start: 0.8348 (pm20) cc_final: 0.8069 (pm20) REVERT: F 63 TYR cc_start: 0.8426 (m-80) cc_final: 0.8152 (m-10) REVERT: G 16 LEU cc_start: 0.8587 (mp) cc_final: 0.8274 (mp) REVERT: G 20 ASP cc_start: 0.7331 (p0) cc_final: 0.7114 (p0) REVERT: G 86 GLN cc_start: 0.8647 (mp10) cc_final: 0.8352 (mm-40) REVERT: I 60 ASP cc_start: 0.7179 (m-30) cc_final: 0.5960 (p0) REVERT: J 86 MET cc_start: 0.7592 (mpp) cc_final: 0.7322 (mpp) REVERT: K 108 ILE cc_start: 0.9264 (mt) cc_final: 0.8984 (mt) REVERT: K 111 ASP cc_start: 0.8740 (t70) cc_final: 0.8485 (t70) REVERT: M 31 LYS cc_start: 0.8679 (tttm) cc_final: 0.8400 (ptmt) REVERT: M 34 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7686 (tt) REVERT: P 50 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8346 (ttmm) REVERT: R 36 ASN cc_start: 0.8524 (t0) cc_final: 0.8213 (t0) REVERT: R 41 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8429 (mtpp) REVERT: S 44 MET cc_start: 0.8459 (mtp) cc_final: 0.8048 (mtm) REVERT: T 42 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8296 (tm-30) REVERT: T 46 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7203 (mm-30) REVERT: T 50 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7115 (pm20) REVERT: T 85 MET cc_start: 0.8428 (mtp) cc_final: 0.8125 (mtm) outliers start: 38 outliers final: 32 residues processed: 367 average time/residue: 0.5165 time to fit residues: 314.6245 Evaluate side-chains 373 residues out of total 2218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 339 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 135 CYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain U residue 128 LEU Chi-restraints excluded: chain U residue 134 THR Chi-restraints excluded: chain U residue 188 MET Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 287 optimal weight: 0.0470 chunk 46 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN G 84 ASN S 47 HIS ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.046572 restraints weight = 151854.646| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 1.30 r_work: 0.2467 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 55042 Z= 0.360 Angle : 0.643 11.063 81211 Z= 0.329 Chirality : 0.039 0.270 10151 Planarity : 0.005 0.051 5125 Dihedral : 23.391 177.165 25169 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 1.98 % Allowed : 17.45 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.01 (0.17), residues: 2595 helix: 1.16 (0.16), residues: 1072 sheet: 0.03 (0.26), residues: 430 loop : -1.20 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 167 HIS 0.007 0.001 HIS N 49 PHE 0.021 0.002 PHE G 62 TYR 0.016 0.002 TYR L 117 ARG 0.009 0.001 ARG F 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7185.46 seconds wall clock time: 129 minutes 0.42 seconds (7740.42 seconds total)