Starting phenix.real_space_refine on Sat Dec 28 00:15:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v2n_31657/12_2024/7v2n_31657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v2n_31657/12_2024/7v2n_31657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v2n_31657/12_2024/7v2n_31657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v2n_31657/12_2024/7v2n_31657.map" model { file = "/net/cci-nas-00/data/ceres_data/7v2n_31657/12_2024/7v2n_31657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v2n_31657/12_2024/7v2n_31657.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.013 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 26613 2.51 5 N 9598 2.21 5 O 13358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51020 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': 125, 'rna2p_pyr': 92, 'rna3p_pur': 665, 'rna3p_pyr': 512} Link IDs: {'rna2p': 216, 'rna3p': 1177} 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: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2088 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 12, 'TRANS': 253} 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 94.160 74.403 94.086 1.00 76.07 S ATOM 33460 SG CYS D 12 95.231 77.300 96.419 1.00 79.67 S ATOM 33578 SG CYS D 26 97.159 73.583 95.112 1.00 84.30 S ATOM 33618 SG CYS D 31 98.207 76.381 93.778 1.00 90.88 S ATOM 44196 SG CYS N 24 62.396 123.021 50.855 1.00130.94 S ATOM 44220 SG CYS N 27 60.733 121.827 54.226 1.00129.77 S ATOM 44327 SG CYS N 40 61.895 125.536 53.706 1.00121.20 S ATOM 44352 SG CYS N 43 64.421 122.864 53.842 1.00119.17 S Time building chain proxies: 21.26, per 1000 atoms: 0.42 Number of scatterers: 51020 At special positions: 0 Unit cell: (142.14, 213.9, 226.32, 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 13358 8.00 N 9598 7.00 C 26613 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: 8.83 Conformation dependent library (CDL) restraints added in 2.9 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 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 21 sheets defined 43.6% alpha, 18.1% beta 398 base pairs and 675 stacking pairs defined. Time for finding SS restraints: 16.91 Creating SS restraints... Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.458A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 65 Processing helix chain 'B' and resid 76 through 87 removed outlier: 4.551A pdb=" N ILE B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.667A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.966A pdb=" N ILE B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.715A pdb=" N SER B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 4.051A pdb=" N LEU B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 155 " --> pdb=" O PHE B 152 " (cutoff:3.500A) No H-bonds generated for '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: 3.889A pdb=" N LEU C 12 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 4.782A pdb=" N ARG C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N HIS C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 removed outlier: 3.515A pdb=" N SER C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.757A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.660A pdb=" N CYS D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.991A 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 99 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.589A pdb=" N GLN D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 190 through 194 Processing helix chain 'D' and resid 199 through 209 removed outlier: 4.015A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.883A 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: 3.647A 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 21 through 31 Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 57 through 68 removed outlier: 4.218A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.521A pdb=" N GLN G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) 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 154 removed outlier: 4.278A pdb=" N HIS G 153 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR G 154 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.636A pdb=" N VAL H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.503A pdb=" N ILE H 100 " --> pdb=" O VAL H 97 " (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 32 through 37 removed outlier: 3.636A pdb=" N PHE I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 47 through 52 removed outlier: 3.704A pdb=" N ARG I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'J' and resid 12 through 30 removed outlier: 3.563A pdb=" N LEU J 16 " --> pdb=" O ASP J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 44 through 49 removed outlier: 4.007A pdb=" N ILE K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.855A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 55 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 removed outlier: 3.662A pdb=" N ALA K 61 " --> pdb=" O THR K 57 " (cutoff:3.500A) 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 removed outlier: 3.571A pdb=" N LEU L 24 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.535A pdb=" N THR M 20 " --> pdb=" O ASP M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.641A pdb=" N TRP M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 16 through 20 removed outlier: 3.515A pdb=" N ARG N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) 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: 3.577A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 4.413A 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 removed outlier: 3.633A pdb=" N ARG P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.223A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.790A pdb=" N SER Q 99 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 26 removed outlier: 3.610A pdb=" N LEU R 26 " --> pdb=" O LYS R 23 " (cutoff:3.500A) 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 77 Processing helix chain 'S' and resid 12 through 24 removed outlier: 4.613A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.635A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.780A pdb=" N ALA T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 92 Processing helix chain 'U' and resid 35 through 45 Processing helix chain 'U' and resid 60 through 70 Processing helix chain 'U' and resid 79 through 84 Proline residue: U 84 - end of helix Processing helix chain 'U' and resid 85 through 90 removed outlier: 3.558A pdb=" N THR U 89 " --> pdb=" O ILE U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 116 removed outlier: 4.149A pdb=" N VAL U 111 " --> pdb=" O ASP U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 143 removed outlier: 3.711A pdb=" N ILE U 136 " --> pdb=" O VAL U 132 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU U 141 " --> pdb=" O ILE U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 Processing helix chain 'U' and resid 220 through 232 removed outlier: 3.589A 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 Processing helix chain 'U' and resid 271 through 275 Processing helix chain 'U' and resid 276 through 289 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: 6.310A pdb=" N PHE B 17 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 42 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B 19 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 3.691A 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: 7.929A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 69 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 186 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 22 removed outlier: 4.112A pdb=" N ARG C 59 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS C 69 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR C 67 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL C 68 " --> pdb=" O GLN C 104 " (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 Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 5.466A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 12 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.608A pdb=" N ILE E 118 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 52 removed outlier: 16.401A pdb=" N VAL F 40 " --> pdb=" O MET F 67 " (cutoff:3.500A) removed outlier: 16.424A pdb=" N MET F 67 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 15.268A pdb=" N GLU F 42 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 15.423A pdb=" N VAL F 65 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 13.597A pdb=" N GLY F 44 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N TYR F 63 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N ARG F 46 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N LEU F 61 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N LEU F 48 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N TYR F 59 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N TYR F 50 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLN F 57 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG F 3 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS F 92 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU F 5 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN F 7 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL F 88 " --> pdb=" O ASN F 7 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 74 through 79 Processing sheet with id=AB1, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB2, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.051A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.509A pdb=" N ARG I 10 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'J' and resid 40 through 49 removed outlier: 4.490A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL J 44 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU J 65 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG J 46 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE J 63 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR J 48 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU J 61 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU J 8 " --> pdb=" O ARG J 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 40 through 49 removed outlier: 4.490A pdb=" N ASN J 69 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR J 42 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR J 67 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL J 44 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU J 65 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG J 46 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE J 63 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR J 48 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU J 61 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.901A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLY K 17 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE K 83 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.536A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE L 97 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR L 66 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.634A pdb=" N ILE P 19 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR P 17 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.742A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.852A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL Q 9 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N LYS Q 69 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU Q 43 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.563A pdb=" N THR S 33 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 99 through 100 removed outlier: 3.683A pdb=" N ILE U 99 " --> pdb=" O ALA U 75 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL U 74 " --> pdb=" O VAL U 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET U 123 " --> pdb=" O GLY U 51 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE U 122 " --> pdb=" O GLY U 149 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N VAL U 151 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL U 124 " --> pdb=" O VAL U 151 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N MET U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER U 203 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE U 189 " --> pdb=" O SER U 203 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL U 205 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE U 209 " --> pdb=" O GLU U 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU U 183 " --> pdb=" O ILE U 209 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1062 hydrogen bonds 1774 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 675 stacking parallelities Total time for adding SS restraints: 28.79 Time building geometry restraints manager: 10.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8894 1.34 - 1.46: 23652 1.46 - 1.58: 19498 1.58 - 1.70: 2785 1.70 - 1.82: 96 Bond restraints: 54925 Sorted by residual: bond pdb=" C ARG D 36 " pdb=" N PRO D 37 " ideal model delta sigma weight residual 1.334 1.358 -0.024 8.40e-03 1.42e+04 8.51e+00 bond pdb=" O5' G A 672 " pdb=" C5' G A 672 " ideal model delta sigma weight residual 1.420 1.460 -0.040 1.50e-02 4.44e+03 6.97e+00 bond pdb=" N GLY U 27 " pdb=" CA GLY U 27 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" C TYR D 38 " pdb=" N PRO D 39 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.18e-02 7.18e+03 6.50e+00 bond pdb=" N GLY D 2 " pdb=" CA GLY D 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.37e+00 ... (remaining 54920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 77200 2.72 - 5.43: 3790 5.43 - 8.15: 62 8.15 - 10.86: 2 10.86 - 13.58: 2 Bond angle restraints: 81056 Sorted by residual: angle pdb=" O3' U A 82 " pdb=" C3' U A 82 " pdb=" C2' U A 82 " ideal model delta sigma weight residual 109.50 123.08 -13.58 1.50e+00 4.44e-01 8.19e+01 angle pdb=" O3' C A 88 " pdb=" C3' C A 88 " pdb=" C2' C A 88 " ideal model delta sigma weight residual 109.50 120.50 -11.00 1.50e+00 4.44e-01 5.38e+01 angle pdb=" O3' A A1269 " pdb=" C3' A A1269 " pdb=" C2' A A1269 " ideal model delta sigma weight residual 109.50 119.39 -9.89 1.50e+00 4.44e-01 4.35e+01 angle pdb=" O3' A A 156 " pdb=" C3' A A 156 " pdb=" C2' A A 156 " ideal model delta sigma weight residual 113.70 122.22 -8.52 1.50e+00 4.44e-01 3.23e+01 angle pdb=" C4' A A1269 " pdb=" C3' A A1269 " pdb=" O3' A A1269 " ideal model delta sigma weight residual 109.40 117.45 -8.05 1.50e+00 4.44e-01 2.88e+01 ... (remaining 81051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 31287 35.94 - 71.88: 3614 71.88 - 107.83: 520 107.83 - 143.77: 17 143.77 - 179.71: 27 Dihedral angle restraints: 35465 sinusoidal: 27915 harmonic: 7550 Sorted by residual: dihedral pdb=" C5' A A1269 " pdb=" C4' A A1269 " pdb=" C3' A A1269 " pdb=" O3' A A1269 " ideal model delta sinusoidal sigma weight residual 147.00 73.21 73.79 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' C A 88 " pdb=" C4' C A 88 " pdb=" C3' C A 88 " pdb=" O3' C A 88 " ideal model delta sinusoidal sigma weight residual 147.00 75.81 71.19 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" O4' C A 20 " pdb=" C1' C A 20 " pdb=" N1 C A 20 " pdb=" C2 C A 20 " ideal model delta sinusoidal sigma weight residual -160.00 19.71 -179.71 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 35462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 8114 0.148 - 0.296: 1994 0.296 - 0.444: 20 0.444 - 0.592: 2 0.592 - 0.740: 3 Chirality restraints: 10133 Sorted by residual: chirality pdb=" C3' C A 88 " pdb=" C4' C A 88 " pdb=" O3' C A 88 " pdb=" C2' C A 88 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' U A 82 " pdb=" C4' U A 82 " pdb=" O3' U A 82 " pdb=" C2' U A 82 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C3' A A1269 " pdb=" C4' A A1269 " pdb=" O3' A A1269 " pdb=" C2' A A1269 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 10130 not shown) Planarity restraints: 5108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1503 " 0.022 2.00e-02 2.50e+03 2.07e-02 1.29e+01 pdb=" N9 G A1503 " -0.015 2.00e-02 2.50e+03 pdb=" C8 G A1503 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G A1503 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1503 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G A1503 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A1503 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G A1503 " 0.046 2.00e-02 2.50e+03 pdb=" C2 G A1503 " -0.042 2.00e-02 2.50e+03 pdb=" N2 G A1503 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1503 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A1503 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 619 " 0.003 2.00e-02 2.50e+03 2.01e-02 1.22e+01 pdb=" N9 G A 619 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G A 619 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 619 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 619 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 619 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G A 619 " 0.027 2.00e-02 2.50e+03 pdb=" N1 G A 619 " -0.046 2.00e-02 2.50e+03 pdb=" C2 G A 619 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G A 619 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 619 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 619 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 864 " -0.006 2.00e-02 2.50e+03 2.00e-02 1.20e+01 pdb=" N9 G A 864 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G A 864 " 0.012 2.00e-02 2.50e+03 pdb=" N7 G A 864 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G A 864 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 864 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A 864 " 0.025 2.00e-02 2.50e+03 pdb=" N1 G A 864 " -0.042 2.00e-02 2.50e+03 pdb=" C2 G A 864 " 0.042 2.00e-02 2.50e+03 pdb=" N2 G A 864 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A 864 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 864 " -0.004 2.00e-02 2.50e+03 ... (remaining 5105 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1463 2.65 - 3.21: 42179 3.21 - 3.77: 99949 3.77 - 4.34: 129093 4.34 - 4.90: 181157 Nonbonded interactions: 453841 Sorted by model distance: nonbonded pdb=" O ASN U 29 " pdb=" OD1 ASN U 29 " model vdw 2.085 3.040 nonbonded pdb=" O2' C A 208 " pdb=" O4' U A 209 " model vdw 2.125 3.040 nonbonded pdb=" ND2 ASN U 29 " pdb=" OH TYR U 130 " model vdw 2.246 3.120 nonbonded pdb=" O2' A A1269 " pdb=" O5' A A1270 " model vdw 2.249 3.040 nonbonded pdb=" O2' A A1232 " pdb=" O4' A A1233 " model vdw 2.270 3.040 ... (remaining 453836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.040 Extract box with map and model: 1.620 Check model and map are aligned: 0.300 Set scattering table: 0.360 Process input model: 110.300 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.130 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 0.042 54925 Z= 0.500 Angle : 1.207 13.576 81056 Z= 0.771 Chirality : 0.111 0.740 10133 Planarity : 0.004 0.021 5108 Dihedral : 24.274 179.710 30607 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.04 % Favored : 92.69 % Rotamer: Outliers : 0.63 % Allowed : 4.85 % Favored : 94.51 % Cbeta Deviations : 0.08 % 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: -1.20 (0.16), residues: 2584 helix: 0.30 (0.15), residues: 994 sheet: -0.68 (0.25), residues: 431 loop : -1.81 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 167 HIS 0.007 0.002 HIS S 14 PHE 0.013 0.002 PHE U 292 TYR 0.014 0.002 TYR U 171 ARG 0.010 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 327 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7493 (tppt) REVERT: B 48 MET cc_start: 0.8555 (mmm) cc_final: 0.8323 (mmm) REVERT: D 33 MET cc_start: 0.7829 (mmm) cc_final: 0.7619 (mmm) REVERT: E 56 GLN cc_start: 0.8229 (mt0) cc_final: 0.8009 (mt0) REVERT: E 76 ILE cc_start: 0.9236 (mm) cc_final: 0.9009 (mt) REVERT: F 15 ASP cc_start: 0.7563 (p0) cc_final: 0.7294 (p0) REVERT: G 43 PHE cc_start: 0.7637 (t80) cc_final: 0.7421 (t80) REVERT: G 109 ASN cc_start: 0.7987 (m110) cc_final: 0.7755 (m110) REVERT: H 42 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8191 (mm-30) REVERT: J 3 LYS cc_start: 0.5155 (ptpt) cc_final: 0.4187 (ttmm) REVERT: J 79 ARG cc_start: 0.6727 (mmp80) cc_final: 0.6493 (mmp80) REVERT: J 90 LEU cc_start: 0.4945 (mp) cc_final: 0.4667 (mm) REVERT: J 95 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6297 (tm-30) REVERT: K 47 VAL cc_start: 0.7391 (t) cc_final: 0.7094 (p) REVERT: K 57 THR cc_start: 0.8085 (m) cc_final: 0.7298 (m) REVERT: K 81 ASP cc_start: 0.6973 (m-30) cc_final: 0.6372 (m-30) REVERT: K 93 GLN cc_start: 0.5299 (pp30) cc_final: 0.4960 (pp30) REVERT: M 4 ILE cc_start: 0.4903 (mm) cc_final: 0.4660 (mt) REVERT: M 21 TYR cc_start: 0.6724 (m-80) cc_final: 0.6476 (m-10) REVERT: N 46 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7620 (mt-10) REVERT: Q 48 GLU cc_start: 0.8350 (mp0) cc_final: 0.8107 (mp0) REVERT: R 21 LYS cc_start: 0.7992 (mttm) cc_final: 0.7737 (mttm) REVERT: S 43 GLU cc_start: 0.7552 (mp0) cc_final: 0.7155 (tm-30) REVERT: S 66 MET cc_start: 0.4410 (ptt) cc_final: 0.4082 (ptt) REVERT: T 90 GLN cc_start: 0.8435 (mp10) cc_final: 0.7777 (mp10) REVERT: U 181 TYR cc_start: 0.7144 (m-10) cc_final: 0.6943 (m-10) REVERT: U 207 ARG cc_start: 0.6067 (ttp-110) cc_final: 0.5681 (ptm160) outliers start: 14 outliers final: 5 residues processed: 341 average time/residue: 0.5836 time to fit residues: 324.2071 Evaluate side-chains 242 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 237 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain T residue 100 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.9990 chunk 297 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 200 optimal weight: 0.0770 chunk 158 optimal weight: 0.9980 chunk 307 optimal weight: 30.0000 chunk 118 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 355 optimal weight: 0.2980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 6 HIS C 63 ASN C 108 ASN C 139 GLN D 119 GLN F 84 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN S 69 HIS U 29 ASN U 144 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 54925 Z= 0.138 Angle : 0.604 8.475 81056 Z= 0.312 Chirality : 0.036 0.416 10133 Planarity : 0.004 0.047 5108 Dihedral : 24.945 178.606 25165 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.64 % Favored : 95.24 % Rotamer: Outliers : 1.04 % Allowed : 9.84 % Favored : 89.12 % 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: -0.42 (0.16), residues: 2584 helix: 1.07 (0.16), residues: 1018 sheet: -0.36 (0.25), residues: 457 loop : -1.52 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.008 0.001 HIS U 144 PHE 0.011 0.001 PHE H 31 TYR 0.024 0.001 TYR U 131 ARG 0.004 0.000 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7231 (tppt) REVERT: C 142 MET cc_start: 0.7563 (mmm) cc_final: 0.7281 (mmt) REVERT: E 76 ILE cc_start: 0.9176 (mm) cc_final: 0.8922 (mt) REVERT: F 23 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8462 (mttm) REVERT: F 55 ASP cc_start: 0.7245 (m-30) cc_final: 0.6897 (t0) REVERT: G 13 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7497 (tm-30) REVERT: G 31 MET cc_start: 0.7172 (tmm) cc_final: 0.6266 (tmm) REVERT: G 85 TYR cc_start: 0.6381 (m-80) cc_final: 0.5368 (m-80) REVERT: J 3 LYS cc_start: 0.5054 (ptpt) cc_final: 0.4514 (ttmm) REVERT: J 95 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6536 (tm-30) REVERT: K 50 TYR cc_start: 0.6738 (m-10) cc_final: 0.6304 (m-10) REVERT: K 59 TYR cc_start: 0.7735 (p90) cc_final: 0.7479 (p90) REVERT: K 81 ASP cc_start: 0.7077 (m-30) cc_final: 0.6669 (m-30) REVERT: O 6 GLU cc_start: 0.8679 (mp0) cc_final: 0.8380 (mp0) REVERT: P 34 GLU cc_start: 0.8536 (tt0) cc_final: 0.8189 (tt0) REVERT: Q 48 GLU cc_start: 0.8414 (mp0) cc_final: 0.8211 (mp0) REVERT: R 21 LYS cc_start: 0.8081 (mttm) cc_final: 0.7845 (mttm) REVERT: R 84 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7784 (mmmt) REVERT: S 43 GLU cc_start: 0.7802 (mp0) cc_final: 0.7199 (tm-30) REVERT: T 90 GLN cc_start: 0.8275 (mp10) cc_final: 0.7800 (tm-30) REVERT: U 52 VAL cc_start: 0.2931 (OUTLIER) cc_final: 0.2565 (p) REVERT: U 123 MET cc_start: 0.3411 (tmm) cc_final: 0.2904 (tmm) REVERT: U 207 ARG cc_start: 0.5896 (ttp-110) cc_final: 0.5547 (ptm160) outliers start: 23 outliers final: 7 residues processed: 293 average time/residue: 0.5180 time to fit residues: 255.0128 Evaluate side-chains 236 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 296 optimal weight: 0.0270 chunk 242 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 356 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 286 optimal weight: 0.0980 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN D 154 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN U 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 54925 Z= 0.149 Angle : 0.559 8.311 81056 Z= 0.289 Chirality : 0.035 0.314 10133 Planarity : 0.004 0.058 5108 Dihedral : 24.777 179.208 25164 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.22 % Favored : 94.66 % Rotamer: Outliers : 1.68 % Allowed : 11.88 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2584 helix: 1.26 (0.16), residues: 1025 sheet: -0.19 (0.26), residues: 451 loop : -1.39 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 167 HIS 0.007 0.001 HIS C 69 PHE 0.015 0.001 PHE G 43 TYR 0.033 0.001 TYR M 21 ARG 0.007 0.000 ARG O 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7628 (tppt) REVERT: B 143 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: E 76 ILE cc_start: 0.9309 (mm) cc_final: 0.9047 (mt) REVERT: G 15 ASP cc_start: 0.6036 (t0) cc_final: 0.5799 (t0) REVERT: G 31 MET cc_start: 0.6927 (tmm) cc_final: 0.5894 (tmm) REVERT: G 85 TYR cc_start: 0.6241 (m-80) cc_final: 0.5376 (m-80) REVERT: G 109 ASN cc_start: 0.7733 (m-40) cc_final: 0.7391 (m110) REVERT: K 50 TYR cc_start: 0.6594 (m-10) cc_final: 0.6195 (m-10) REVERT: K 81 ASP cc_start: 0.6930 (m-30) cc_final: 0.6543 (m-30) REVERT: O 74 ASP cc_start: 0.7747 (t0) cc_final: 0.7327 (t0) REVERT: P 34 GLU cc_start: 0.8527 (tt0) cc_final: 0.8159 (tt0) REVERT: P 47 ASP cc_start: 0.8499 (p0) cc_final: 0.8248 (p0) REVERT: P 52 ASP cc_start: 0.8143 (t0) cc_final: 0.7887 (t0) REVERT: Q 48 GLU cc_start: 0.8531 (mp0) cc_final: 0.8304 (mp0) REVERT: R 21 LYS cc_start: 0.7962 (mttm) cc_final: 0.7684 (mttm) REVERT: R 84 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7806 (mmmt) REVERT: S 43 GLU cc_start: 0.7641 (mp0) cc_final: 0.7010 (tm-30) REVERT: S 62 ILE cc_start: 0.7666 (mm) cc_final: 0.7074 (tt) REVERT: T 90 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: U 52 VAL cc_start: 0.2843 (OUTLIER) cc_final: 0.2518 (p) REVERT: U 123 MET cc_start: 0.3413 (tmm) cc_final: 0.2949 (tmm) outliers start: 37 outliers final: 21 residues processed: 277 average time/residue: 0.4884 time to fit residues: 228.9646 Evaluate side-chains 247 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 0.3980 chunk 239 optimal weight: 20.0000 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 339 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN O 37 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54925 Z= 0.241 Angle : 0.602 9.004 81056 Z= 0.308 Chirality : 0.037 0.302 10133 Planarity : 0.005 0.055 5108 Dihedral : 24.755 179.649 25164 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 1.59 % Allowed : 13.70 % Favored : 84.72 % 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: -0.18 (0.17), residues: 2584 helix: 1.25 (0.16), residues: 1022 sheet: -0.25 (0.26), residues: 446 loop : -1.36 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 138 HIS 0.007 0.001 HIS G 122 PHE 0.009 0.001 PHE U 30 TYR 0.022 0.002 TYR I 114 ARG 0.006 0.000 ARG O 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7612 (tppt) REVERT: D 33 MET cc_start: 0.7875 (mmm) cc_final: 0.7663 (mmm) REVERT: E 76 ILE cc_start: 0.9295 (mm) cc_final: 0.9062 (mt) REVERT: G 31 MET cc_start: 0.6968 (tmm) cc_final: 0.6055 (tmm) REVERT: G 73 MET cc_start: 0.6387 (tpp) cc_final: 0.6181 (tpp) REVERT: J 3 LYS cc_start: 0.5631 (tppt) cc_final: 0.4943 (ttmm) REVERT: J 95 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6277 (tm-30) REVERT: K 81 ASP cc_start: 0.6820 (m-30) cc_final: 0.6442 (m-30) REVERT: M 3 ARG cc_start: 0.4659 (mmp-170) cc_final: 0.3751 (tmm160) REVERT: M 4 ILE cc_start: 0.5424 (mm) cc_final: 0.4286 (mt) REVERT: M 32 GLU cc_start: 0.7550 (pp20) cc_final: 0.7244 (pp20) REVERT: O 74 ASP cc_start: 0.7760 (t0) cc_final: 0.7336 (t0) REVERT: P 47 ASP cc_start: 0.8605 (p0) cc_final: 0.8269 (p0) REVERT: P 52 ASP cc_start: 0.8047 (t0) cc_final: 0.7814 (t0) REVERT: R 21 LYS cc_start: 0.8091 (mttm) cc_final: 0.7803 (mttm) REVERT: S 43 GLU cc_start: 0.7519 (mp0) cc_final: 0.6927 (tm-30) REVERT: T 90 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: U 52 VAL cc_start: 0.2868 (OUTLIER) cc_final: 0.2552 (p) REVERT: U 123 MET cc_start: 0.3481 (tmm) cc_final: 0.2999 (tmm) REVERT: U 153 MET cc_start: 0.7985 (ppp) cc_final: 0.7715 (ppp) REVERT: U 198 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6442 (mm-40) outliers start: 35 outliers final: 28 residues processed: 260 average time/residue: 0.4939 time to fit residues: 218.1546 Evaluate side-chains 254 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 198 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 340 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN O 13 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 54925 Z= 0.352 Angle : 0.689 8.478 81056 Z= 0.350 Chirality : 0.040 0.266 10133 Planarity : 0.006 0.056 5108 Dihedral : 24.859 179.516 25164 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 2.63 % Allowed : 14.38 % Favored : 82.99 % 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: -0.55 (0.17), residues: 2584 helix: 0.90 (0.16), residues: 1044 sheet: -0.60 (0.25), residues: 446 loop : -1.49 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 138 HIS 0.008 0.002 HIS G 122 PHE 0.015 0.002 PHE H 31 TYR 0.027 0.002 TYR K 50 ARG 0.007 0.001 ARG T 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7400 (tppt) REVERT: C 15 THR cc_start: 0.7537 (p) cc_final: 0.7270 (t) REVERT: E 76 ILE cc_start: 0.9240 (mm) cc_final: 0.8971 (mt) REVERT: F 1 MET cc_start: 0.6517 (ttt) cc_final: 0.6309 (ttt) REVERT: G 15 ASP cc_start: 0.5831 (t0) cc_final: 0.5511 (t0) REVERT: G 31 MET cc_start: 0.7110 (tmm) cc_final: 0.6202 (tmm) REVERT: J 3 LYS cc_start: 0.5310 (tppt) cc_final: 0.4926 (ttmm) REVERT: J 95 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6242 (tm-30) REVERT: K 81 ASP cc_start: 0.6691 (m-30) cc_final: 0.6395 (m-30) REVERT: K 87 THR cc_start: 0.8213 (t) cc_final: 0.7805 (p) REVERT: M 3 ARG cc_start: 0.4548 (mmp-170) cc_final: 0.3716 (tmm160) REVERT: M 4 ILE cc_start: 0.5523 (mm) cc_final: 0.4379 (mt) REVERT: O 6 GLU cc_start: 0.8504 (mp0) cc_final: 0.8274 (mp0) REVERT: O 74 ASP cc_start: 0.7789 (t0) cc_final: 0.7366 (t0) REVERT: P 47 ASP cc_start: 0.8731 (p0) cc_final: 0.8446 (p0) REVERT: P 52 ASP cc_start: 0.8260 (t0) cc_final: 0.8055 (t0) REVERT: R 21 LYS cc_start: 0.8311 (mttm) cc_final: 0.8035 (mttm) REVERT: S 43 GLU cc_start: 0.7538 (mp0) cc_final: 0.6727 (tm-30) REVERT: T 90 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: U 65 GLN cc_start: 0.6127 (OUTLIER) cc_final: 0.5780 (mp10) REVERT: U 123 MET cc_start: 0.3849 (tmm) cc_final: 0.3434 (tmm) REVERT: U 181 TYR cc_start: 0.7432 (m-10) cc_final: 0.7147 (m-10) REVERT: U 198 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6310 (mt0) outliers start: 58 outliers final: 42 residues processed: 265 average time/residue: 0.4862 time to fit residues: 218.3180 Evaluate side-chains 257 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 30.0000 chunk 341 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 379 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN S 69 HIS ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 54925 Z= 0.384 Angle : 0.711 8.562 81056 Z= 0.360 Chirality : 0.042 0.275 10133 Planarity : 0.006 0.056 5108 Dihedral : 24.904 179.827 25164 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 2.90 % Allowed : 15.10 % Favored : 82.00 % 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: -0.76 (0.16), residues: 2584 helix: 0.71 (0.16), residues: 1045 sheet: -0.79 (0.25), residues: 427 loop : -1.54 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 138 HIS 0.007 0.002 HIS G 122 PHE 0.018 0.002 PHE C 10 TYR 0.021 0.002 TYR K 50 ARG 0.006 0.001 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7397 (tppt) REVERT: B 48 MET cc_start: 0.8448 (mmm) cc_final: 0.8173 (mmm) REVERT: B 55 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: C 15 THR cc_start: 0.7525 (p) cc_final: 0.7257 (t) REVERT: C 201 TYR cc_start: 0.6512 (m-80) cc_final: 0.6078 (m-80) REVERT: E 76 ILE cc_start: 0.9251 (mm) cc_final: 0.8975 (mt) REVERT: F 50 TYR cc_start: 0.8027 (p90) cc_final: 0.7632 (p90) REVERT: G 15 ASP cc_start: 0.6037 (t0) cc_final: 0.5624 (t0) REVERT: G 31 MET cc_start: 0.7444 (tmm) cc_final: 0.6794 (tmm) REVERT: G 73 MET cc_start: 0.6669 (tpp) cc_final: 0.6448 (tpp) REVERT: J 3 LYS cc_start: 0.5356 (tppt) cc_final: 0.4962 (ttmm) REVERT: J 95 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6278 (tm-30) REVERT: K 81 ASP cc_start: 0.6607 (m-30) cc_final: 0.6366 (m-30) REVERT: K 87 THR cc_start: 0.8251 (t) cc_final: 0.7819 (p) REVERT: M 3 ARG cc_start: 0.4205 (mmp-170) cc_final: 0.3482 (tmm160) REVERT: M 4 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.4961 (mt) REVERT: N 46 GLU cc_start: 0.8048 (mt-10) cc_final: 0.6847 (mp0) REVERT: O 6 GLU cc_start: 0.8437 (mp0) cc_final: 0.8179 (mp0) REVERT: O 74 ASP cc_start: 0.8010 (t0) cc_final: 0.7486 (t0) REVERT: R 21 LYS cc_start: 0.8425 (mttm) cc_final: 0.8130 (mttm) REVERT: R 42 ARG cc_start: 0.8580 (tpp80) cc_final: 0.7920 (mtp85) REVERT: S 43 GLU cc_start: 0.7527 (mp0) cc_final: 0.6636 (tm-30) REVERT: T 90 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: U 65 GLN cc_start: 0.5926 (OUTLIER) cc_final: 0.5598 (mp10) REVERT: U 181 TYR cc_start: 0.7395 (m-10) cc_final: 0.7131 (m-10) REVERT: U 198 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6383 (mt0) outliers start: 64 outliers final: 44 residues processed: 266 average time/residue: 0.5092 time to fit residues: 228.7169 Evaluate side-chains 257 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 377 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54925 Z= 0.199 Angle : 0.597 8.908 81056 Z= 0.305 Chirality : 0.036 0.262 10133 Planarity : 0.004 0.054 5108 Dihedral : 24.807 179.383 25164 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 2.13 % Allowed : 16.60 % Favored : 81.27 % 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: -0.37 (0.17), residues: 2584 helix: 1.10 (0.16), residues: 1037 sheet: -0.50 (0.26), residues: 411 loop : -1.43 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.012 0.001 PHE C 10 TYR 0.022 0.001 TYR K 50 ARG 0.003 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7470 (tppt) REVERT: C 6 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.6226 (t70) REVERT: C 15 THR cc_start: 0.7504 (p) cc_final: 0.7246 (t) REVERT: C 201 TYR cc_start: 0.6503 (m-80) cc_final: 0.6283 (m-80) REVERT: E 76 ILE cc_start: 0.9282 (mm) cc_final: 0.9022 (mt) REVERT: F 50 TYR cc_start: 0.7971 (p90) cc_final: 0.7658 (p90) REVERT: G 31 MET cc_start: 0.7474 (tmm) cc_final: 0.6841 (tmm) REVERT: G 73 MET cc_start: 0.6672 (tpp) cc_final: 0.6364 (tpp) REVERT: H 37 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8033 (ptp-110) REVERT: J 3 LYS cc_start: 0.5266 (tppt) cc_final: 0.4935 (ttmm) REVERT: J 95 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6243 (tm-30) REVERT: K 77 MET cc_start: 0.6986 (mmm) cc_final: 0.6548 (mmp) REVERT: K 81 ASP cc_start: 0.6618 (m-30) cc_final: 0.6376 (m-30) REVERT: M 3 ARG cc_start: 0.4268 (mmp-170) cc_final: 0.3549 (tmm160) REVERT: N 46 GLU cc_start: 0.8043 (mt-10) cc_final: 0.6791 (mp0) REVERT: O 6 GLU cc_start: 0.8474 (mp0) cc_final: 0.8222 (mp0) REVERT: O 74 ASP cc_start: 0.7722 (t0) cc_final: 0.7186 (t0) REVERT: R 21 LYS cc_start: 0.8416 (mttm) cc_final: 0.8118 (mttm) REVERT: S 43 GLU cc_start: 0.7545 (mp0) cc_final: 0.6625 (tm-30) REVERT: S 66 MET cc_start: 0.2954 (mmt) cc_final: 0.2691 (tpp) REVERT: T 90 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: U 123 MET cc_start: 0.4218 (ttp) cc_final: 0.3399 (tmm) REVERT: U 181 TYR cc_start: 0.7212 (m-10) cc_final: 0.6765 (m-10) REVERT: U 198 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6473 (mt0) outliers start: 47 outliers final: 33 residues processed: 257 average time/residue: 0.5128 time to fit residues: 223.5296 Evaluate side-chains 244 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 296 optimal weight: 0.6980 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 54925 Z= 0.386 Angle : 0.714 9.438 81056 Z= 0.360 Chirality : 0.041 0.251 10133 Planarity : 0.006 0.056 5108 Dihedral : 24.855 179.706 25160 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.04 % Favored : 92.84 % Rotamer: Outliers : 2.72 % Allowed : 16.96 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2584 helix: 0.82 (0.16), residues: 1042 sheet: -0.57 (0.26), residues: 417 loop : -1.49 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 138 HIS 0.009 0.001 HIS G 122 PHE 0.011 0.002 PHE U 195 TYR 0.027 0.002 TYR K 50 ARG 0.008 0.001 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7459 (tppt) REVERT: B 48 MET cc_start: 0.8392 (mmm) cc_final: 0.8169 (mmm) REVERT: C 6 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.6316 (t70) REVERT: C 15 THR cc_start: 0.7533 (p) cc_final: 0.7292 (t) REVERT: C 17 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6444 (t0) REVERT: C 201 TYR cc_start: 0.6494 (m-80) cc_final: 0.6078 (m-80) REVERT: E 76 ILE cc_start: 0.9312 (mm) cc_final: 0.9003 (mt) REVERT: F 15 ASP cc_start: 0.7627 (p0) cc_final: 0.7200 (p0) REVERT: F 50 TYR cc_start: 0.8066 (p90) cc_final: 0.7707 (p90) REVERT: G 31 MET cc_start: 0.7472 (tmm) cc_final: 0.6779 (tmm) REVERT: H 37 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8096 (ptp-110) REVERT: J 95 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6279 (tm-30) REVERT: K 81 ASP cc_start: 0.6639 (m-30) cc_final: 0.6410 (m-30) REVERT: M 3 ARG cc_start: 0.4061 (mmp-170) cc_final: 0.3407 (tmm160) REVERT: N 8 GLU cc_start: 0.4892 (OUTLIER) cc_final: 0.3767 (tm-30) REVERT: N 46 GLU cc_start: 0.8038 (mt-10) cc_final: 0.6837 (mp0) REVERT: O 6 GLU cc_start: 0.8515 (mp0) cc_final: 0.8220 (mp0) REVERT: O 74 ASP cc_start: 0.8003 (t0) cc_final: 0.7461 (t0) REVERT: P 34 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: R 21 LYS cc_start: 0.8366 (mttm) cc_final: 0.8048 (mttm) REVERT: S 43 GLU cc_start: 0.7488 (mp0) cc_final: 0.6913 (mp0) REVERT: S 66 MET cc_start: 0.3111 (mmt) cc_final: 0.2789 (tpp) REVERT: T 90 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: U 65 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5903 (mp10) REVERT: U 181 TYR cc_start: 0.7478 (m-10) cc_final: 0.7187 (m-10) REVERT: U 198 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6511 (mt0) outliers start: 60 outliers final: 46 residues processed: 255 average time/residue: 0.5035 time to fit residues: 215.9376 Evaluate side-chains 256 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 92 HIS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain Q residue 83 ASP Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.9990 chunk 361 optimal weight: 10.0000 chunk 330 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 54925 Z= 0.223 Angle : 0.615 10.147 81056 Z= 0.313 Chirality : 0.037 0.230 10133 Planarity : 0.005 0.055 5108 Dihedral : 24.796 179.004 25160 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 2.36 % Allowed : 17.55 % Favored : 80.09 % 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: -0.41 (0.17), residues: 2584 helix: 1.06 (0.16), residues: 1036 sheet: -0.54 (0.26), residues: 400 loop : -1.41 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 138 HIS 0.007 0.001 HIS G 122 PHE 0.012 0.001 PHE G 62 TYR 0.020 0.002 TYR K 50 ARG 0.007 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7232 (tppt) REVERT: B 55 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: C 6 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.6287 (t70) REVERT: C 15 THR cc_start: 0.7442 (p) cc_final: 0.7226 (t) REVERT: C 17 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6292 (t0) REVERT: C 77 ILE cc_start: 0.5075 (mm) cc_final: 0.4690 (tp) REVERT: C 201 TYR cc_start: 0.6412 (m-80) cc_final: 0.6013 (m-80) REVERT: E 76 ILE cc_start: 0.9293 (mm) cc_final: 0.9019 (mt) REVERT: F 50 TYR cc_start: 0.7987 (p90) cc_final: 0.7627 (p90) REVERT: G 31 MET cc_start: 0.7586 (tmm) cc_final: 0.6939 (tmm) REVERT: H 37 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8063 (ptp-110) REVERT: J 95 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6255 (tm-30) REVERT: K 81 ASP cc_start: 0.6652 (m-30) cc_final: 0.6434 (m-30) REVERT: M 3 ARG cc_start: 0.4033 (mmp-170) cc_final: 0.3372 (tmm160) REVERT: N 46 GLU cc_start: 0.7972 (mt-10) cc_final: 0.6813 (mp0) REVERT: O 6 GLU cc_start: 0.8531 (mp0) cc_final: 0.8256 (mp0) REVERT: O 74 ASP cc_start: 0.7779 (t0) cc_final: 0.7244 (t0) REVERT: R 21 LYS cc_start: 0.8422 (mttm) cc_final: 0.8114 (mttm) REVERT: S 43 GLU cc_start: 0.7637 (mp0) cc_final: 0.6623 (tm-30) REVERT: T 90 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: U 65 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5780 (mp10) REVERT: U 153 MET cc_start: 0.7541 (ppp) cc_final: 0.7322 (ppp) REVERT: U 181 TYR cc_start: 0.7238 (m-10) cc_final: 0.6822 (m-10) REVERT: U 198 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6471 (mt0) outliers start: 52 outliers final: 42 residues processed: 255 average time/residue: 0.5057 time to fit residues: 216.8279 Evaluate side-chains 257 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 20.0000 chunk 372 optimal weight: 0.2980 chunk 227 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 258 optimal weight: 6.9990 chunk 390 optimal weight: 30.0000 chunk 359 optimal weight: 5.9990 chunk 310 optimal weight: 0.0020 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 overall best weight: 4.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 GLN G 97 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54925 Z= 0.249 Angle : 0.625 11.255 81056 Z= 0.318 Chirality : 0.037 0.223 10133 Planarity : 0.005 0.056 5108 Dihedral : 24.780 179.370 25160 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 2.63 % Allowed : 17.51 % Favored : 79.86 % 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: -0.40 (0.17), residues: 2584 helix: 1.03 (0.16), residues: 1036 sheet: -0.50 (0.26), residues: 391 loop : -1.39 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.010 0.001 PHE D 79 TYR 0.019 0.002 TYR I 92 ARG 0.007 0.000 ARG K 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7307 (tppt) REVERT: B 55 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: C 6 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6284 (t70) REVERT: C 15 THR cc_start: 0.7435 (p) cc_final: 0.7223 (t) REVERT: C 17 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6291 (t0) REVERT: C 77 ILE cc_start: 0.4911 (mm) cc_final: 0.4554 (tp) REVERT: C 139 GLN cc_start: 0.8796 (tt0) cc_final: 0.8227 (pp30) REVERT: C 201 TYR cc_start: 0.6428 (m-80) cc_final: 0.6022 (m-80) REVERT: E 76 ILE cc_start: 0.9292 (mm) cc_final: 0.9018 (mt) REVERT: F 50 TYR cc_start: 0.7989 (p90) cc_final: 0.7608 (p90) REVERT: G 84 ASN cc_start: 0.6314 (m-40) cc_final: 0.6091 (m-40) REVERT: H 37 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8097 (ptp-110) REVERT: J 95 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6257 (tm-30) REVERT: K 81 ASP cc_start: 0.6637 (m-30) cc_final: 0.6414 (m-30) REVERT: M 3 ARG cc_start: 0.3853 (mmp-170) cc_final: 0.3245 (tmm160) REVERT: N 46 GLU cc_start: 0.7988 (mt-10) cc_final: 0.6826 (mp0) REVERT: O 6 GLU cc_start: 0.8490 (mp0) cc_final: 0.8175 (mp0) REVERT: O 74 ASP cc_start: 0.7803 (t0) cc_final: 0.7268 (t0) REVERT: P 34 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: R 21 LYS cc_start: 0.8353 (mttm) cc_final: 0.7993 (mttm) REVERT: S 43 GLU cc_start: 0.7499 (mp0) cc_final: 0.6560 (tm-30) REVERT: T 90 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: U 65 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5774 (mp10) REVERT: U 153 MET cc_start: 0.7465 (ppp) cc_final: 0.7180 (ppp) REVERT: U 181 TYR cc_start: 0.7287 (m-10) cc_final: 0.6869 (m-10) REVERT: U 198 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6509 (mt0) outliers start: 58 outliers final: 44 residues processed: 254 average time/residue: 0.5075 time to fit residues: 216.8514 Evaluate side-chains 259 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 130 TYR Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 207 ARG Chi-restraints excluded: chain U residue 279 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 6.9990 chunk 331 optimal weight: 0.9990 chunk 95 optimal weight: 30.0000 chunk 286 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 319 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN D 160 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.041740 restraints weight = 264328.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042412 restraints weight = 142431.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.042156 restraints weight = 96970.138| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 54925 Z= 0.305 Angle : 0.657 11.039 81056 Z= 0.333 Chirality : 0.039 0.230 10133 Planarity : 0.005 0.056 5108 Dihedral : 24.788 179.957 25160 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 2.54 % Allowed : 17.78 % Favored : 79.68 % 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: -0.46 (0.17), residues: 2584 helix: 0.97 (0.16), residues: 1036 sheet: -0.55 (0.26), residues: 392 loop : -1.39 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 138 HIS 0.008 0.001 HIS G 122 PHE 0.010 0.002 PHE C 10 TYR 0.019 0.002 TYR K 50 ARG 0.008 0.001 ARG D 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.28 seconds wall clock time: 104 minutes 24.11 seconds (6264.11 seconds total)