Starting phenix.real_space_refine on Sat Oct 31 03:45:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.cif Found real_map, /net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.cif" model { file = "/net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6swd_10323/10_2026/6swd_10323.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 1064 5.49 5 Mg 25 5.21 5 S 61 5.16 5 C 22047 2.51 5 N 7689 2.21 5 O 10657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41548 Number of models: 1 Model: "" Number of chains: 28 Chain: "2" Number of atoms: 22543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 22543 Classifications: {'RNA': 32, 'RNAv2': 1012} Modifications used: {'rna2p': 1, 'rna2p_pur': 77, 'rna2p_pyr': 45, 'rna3p': 30, 'rna3p_pur': 511, 'rna3p_pyr': 379} Link IDs: {'rna2p': 123, 'rna3p': 920} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1533 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1470 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1983 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 18, 'TRANS': 223} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "M" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "Q" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1262 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "R" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 900 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 790 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "W" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "0" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 343 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "5" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "6" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Unusual residues: {' MG': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25886 SG CYS C 32 65.350 150.459 94.325 1.00 26.53 S ATOM 25907 SG CYS C 35 63.052 152.482 95.695 1.00 35.19 S ATOM 26069 SG CYS C 55 65.678 149.485 97.389 1.00 37.23 S ATOM 26091 SG CYS C 58 61.726 151.071 96.423 1.00 42.19 S ATOM 25745 SG CYS C 14 71.741 137.444 96.265 1.00 22.39 S ATOM 25764 SG CYS C 17 71.556 134.045 98.420 1.00 23.72 S ATOM 25972 SG CYS C 43 73.188 134.115 94.697 1.00 20.55 S ATOM 25994 SG CYS C 46 70.779 133.981 94.859 1.00 20.68 S ATOM 30604 SG CYS F 128 95.448 126.429 114.423 1.00 8.55 S ATOM 30643 SG CYS F 133 98.211 125.450 116.334 1.00 11.68 S ATOM 30660 SG CYS F 135 98.180 128.404 116.099 1.00 13.01 S ATOM 37888 SG CYS R 16 58.699 68.946 146.473 1.00 39.38 S ATOM 37926 SG CYS R 21 62.074 70.021 146.831 1.00 26.42 S ATOM 38414 SG CYS R 77 58.482 70.616 145.034 1.00 32.53 S ATOM 39617 SG CYS W 20 10.102 113.011 94.632 1.00 38.38 S ATOM 39639 SG CYS W 23 7.943 110.695 95.605 1.00 48.30 S ATOM 39765 SG CYS W 39 11.239 109.988 97.806 1.00 41.92 S ATOM 39786 SG CYS W 42 8.868 109.202 95.609 1.00 45.75 S Time building chain proxies: 7.71, per 1000 atoms: 0.19 Number of scatterers: 41548 At special positions: 0 Unit cell: (168.95, 177.67, 207.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 61 16.00 P 1064 15.00 Mg 25 11.99 O 10657 8.00 N 7689 7.00 C 22047 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 934.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 23 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " Number of angles added : 24 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 34 sheets defined 25.9% alpha, 20.9% beta 264 base pairs and 583 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 removed outlier: 3.566A pdb=" N LEU A 16 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.697A pdb=" N ALA A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.542A pdb=" N LEU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 175 removed outlier: 4.456A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.504A pdb=" N LYS B 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 30 " --> pdb=" O ASP B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 30' Processing helix chain 'B' and resid 45 through 60 removed outlier: 4.139A pdb=" N VAL B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.528A pdb=" N THR B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.657A pdb=" N TYR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.918A pdb=" N PHE B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.767A pdb=" N LEU C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 34 removed outlier: 3.990A pdb=" N ARG D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.652A pdb=" N LYS D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.919A pdb=" N ALA D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 80 removed outlier: 3.861A pdb=" N GLU D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 117 through 127 removed outlier: 3.639A pdb=" N ALA D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.559A pdb=" N VAL E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.950A pdb=" N ASN E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.939A pdb=" N TYR F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA F 9 " --> pdb=" O TRP F 5 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS F 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.642A pdb=" N ILE F 37 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.504A pdb=" N LEU F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 58 removed outlier: 3.656A pdb=" N ASN F 58 " --> pdb=" O PRO F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 58' Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.730A pdb=" N LYS F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.593A pdb=" N ILE F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 208 Processing helix chain 'F' and resid 214 through 222 removed outlier: 3.993A pdb=" N ILE F 218 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.567A pdb=" N GLU G 27 " --> pdb=" O PRO G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'I' and resid 5 through 18 removed outlier: 3.647A pdb=" N ASN I 9 " --> pdb=" O ASP I 5 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 44 removed outlier: 3.683A pdb=" N VAL I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR I 44 " --> pdb=" O VAL I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 94 removed outlier: 4.101A pdb=" N ARG I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 120 removed outlier: 3.922A pdb=" N GLU I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 26 No H-bonds generated for 'chain 'J' and resid 24 through 26' Processing helix chain 'J' and resid 88 through 93 removed outlier: 4.026A pdb=" N ARG J 92 " --> pdb=" O GLN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'M' and resid 56 through 75 removed outlier: 4.019A pdb=" N GLU M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY M 75 " --> pdb=" O ALA M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 removed outlier: 3.550A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 24 removed outlier: 3.705A pdb=" N LEU N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 27 No H-bonds generated for 'chain 'N' and resid 25 through 27' Processing helix chain 'N' and resid 30 through 35 Processing helix chain 'N' and resid 92 through 97 removed outlier: 3.617A pdb=" N LYS N 95 " --> pdb=" O GLY N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 114 Processing helix chain 'N' and resid 134 through 139 removed outlier: 3.580A pdb=" N LYS N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 42 removed outlier: 3.556A pdb=" N LEU Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Q 41 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS Q 42 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 removed outlier: 4.362A pdb=" N GLY Q 51 " --> pdb=" O THR Q 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE Q 53 " --> pdb=" O MET Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 83 Processing helix chain 'Q' and resid 92 through 101 Processing helix chain 'Q' and resid 118 through 139 removed outlier: 3.715A pdb=" N GLN Q 123 " --> pdb=" O MET Q 119 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR Q 135 " --> pdb=" O ARG Q 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 44 removed outlier: 3.514A pdb=" N VAL V 36 " --> pdb=" O SER V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 82 removed outlier: 3.663A pdb=" N MET V 78 " --> pdb=" O ASP V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 90 removed outlier: 4.332A pdb=" N LEU V 87 " --> pdb=" O PRO V 83 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 33 removed outlier: 3.796A pdb=" N LYS 0 21 " --> pdb=" O LYS 0 17 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG 0 22 " --> pdb=" O TRP 0 18 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG 0 25 " --> pdb=" O LYS 0 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 0 26 " --> pdb=" O ARG 0 22 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS 0 31 " --> pdb=" O LYS 0 27 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 97 removed outlier: 4.276A pdb=" N ARG 6 96 " --> pdb=" O ASP 6 92 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS 6 97 " --> pdb=" O TRP 6 93 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 92 through 97' Processing helix chain '6' and resid 101 through 105 removed outlier: 3.723A pdb=" N PHE 6 104 " --> pdb=" O THR 6 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.039A pdb=" N GLY A 34 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA A 79 " --> pdb=" O TRP A 19 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 21 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 73 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.707A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ARG A 187 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET A 121 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE A 189 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 119 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 191 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LYS A 117 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 106 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.925A pdb=" N VAL B 42 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.653A pdb=" N ALA B 69 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 68 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AA6, first strand: chain 'D' and resid 130 through 132 removed outlier: 3.638A pdb=" N THR D 153 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 77 removed outlier: 3.512A pdb=" N ARG E 76 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 98 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 104 removed outlier: 3.829A pdb=" N LEU E 103 " --> pdb=" O ILE E 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 150 removed outlier: 4.041A pdb=" N LEU E 165 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU E 175 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS E 167 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE E 173 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 222 through 226 removed outlier: 6.838A pdb=" N VAL E 212 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 75 removed outlier: 5.466A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 67 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY F 103 " --> pdb=" O PHE F 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 75 removed outlier: 5.466A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 67 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 125 through 126 Processing sheet with id=AB6, first strand: chain 'F' and resid 145 through 149 Processing sheet with id=AB7, first strand: chain 'G' and resid 16 through 22 removed outlier: 7.950A pdb=" N VAL G 119 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS G 5 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL G 121 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL G 7 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU G 123 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER G 9 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN G 120 " --> pdb=" O ARG G 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 122 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 83 through 88 Processing sheet with id=AB9, first strand: chain 'I' and resid 24 through 27 removed outlier: 3.529A pdb=" N GLN I 64 " --> pdb=" O GLU I 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 49 " --> pdb=" O GLN I 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 71 through 74 removed outlier: 3.814A pdb=" N LYS I 71 " --> pdb=" O TYR I 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 71 through 74 removed outlier: 3.814A pdb=" N LYS I 71 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG I 124 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE I 101 " --> pdb=" O TYR I 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 3 through 4 removed outlier: 4.393A pdb=" N ILE J 3 " --> pdb=" O GLY J 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 36 through 37 removed outlier: 6.600A pdb=" N ARG J 36 " --> pdb=" O ALA J 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 43 through 47 Processing sheet with id=AC6, first strand: chain 'J' and resid 65 through 66 removed outlier: 3.770A pdb=" N ILE J 100 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG J 79 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 38 through 43 removed outlier: 6.392A pdb=" N VAL M 79 " --> pdb=" O ILE M 112 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG M 114 " --> pdb=" O VAL M 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 132 through 133 removed outlier: 5.660A pdb=" N VAL N 126 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU N 106 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS N 128 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL N 54 " --> pdb=" O GLN N 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN N 76 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU N 56 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N TYR N 124 " --> pdb=" O VAL N 83 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR N 85 " --> pdb=" O TYR N 124 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL N 126 " --> pdb=" O THR N 85 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE N 87 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N LYS N 128 " --> pdb=" O PHE N 87 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 67 through 68 removed outlier: 3.512A pdb=" N ASP Q 68 " --> pdb=" O ARG Q 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG Q 74 " --> pdb=" O ASP Q 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'R' and resid 33 through 40 removed outlier: 17.826A pdb=" N VAL R 33 " --> pdb=" O TYR R 54 " (cutoff:3.500A) removed outlier: 15.075A pdb=" N TYR R 54 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N GLU R 35 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN R 52 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR R 48 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N PHE R 100 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS R 71 " --> pdb=" O PHE R 100 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL R 102 " --> pdb=" O HIS R 71 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS R 73 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA R 104 " --> pdb=" O HIS R 73 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL R 102 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA R 89 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 104 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 88 " --> pdb=" O PHE R 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 2 through 3 Processing sheet with id=AD3, first strand: chain 'V' and resid 2 through 3 removed outlier: 3.814A pdb=" N PHE V 21 " --> pdb=" O GLY V 67 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY V 67 " --> pdb=" O PHE V 21 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR V 51 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 15 through 16 Processing sheet with id=AD5, first strand: chain 'W' and resid 18 through 19 Processing sheet with id=AD6, first strand: chain '6' and resid 24 through 27 removed outlier: 3.780A pdb=" N TYR 6 84 " --> pdb=" O ILE 6 68 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 37 through 40 521 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 715 hydrogen bonds 1256 hydrogen bond angles 0 basepair planarities 264 basepair parallelities 583 stacking parallelities Total time for adding SS restraints: 13.68 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4038 1.28 - 1.42: 17237 1.42 - 1.55: 21069 1.55 - 1.68: 2129 1.68 - 1.81: 101 Bond restraints: 44574 Sorted by residual: bond pdb=" C4 5HM 21378 " pdb=" N4 5HM 21378 " ideal model delta sigma weight residual 1.338 1.474 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" P A2M 2 373 " pdb=" O5' A2M 2 373 " ideal model delta sigma weight residual 1.722 1.588 0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C5 5HM 21378 " pdb=" C6 5HM 21378 " ideal model delta sigma weight residual 1.349 1.483 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" N3 5HM 21378 " pdb=" C4 5HM 21378 " ideal model delta sigma weight residual 1.319 1.441 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C2 5HM 21378 " pdb=" N3 5HM 21378 " ideal model delta sigma weight residual 1.348 1.466 -0.118 2.00e-02 2.50e+03 3.48e+01 ... (remaining 44569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 60766 2.26 - 4.51: 3806 4.51 - 6.77: 631 6.77 - 9.03: 57 9.03 - 11.28: 13 Bond angle restraints: 65273 Sorted by residual: angle pdb=" C CYS 6 41 " pdb=" N GLU 6 42 " pdb=" CA GLU 6 42 " ideal model delta sigma weight residual 122.73 114.96 7.77 1.61e+00 3.86e-01 2.33e+01 angle pdb=" N VAL W 63 " pdb=" CA VAL W 63 " pdb=" C VAL W 63 " ideal model delta sigma weight residual 113.47 108.73 4.74 1.01e+00 9.80e-01 2.20e+01 angle pdb=" N GLY F 171 " pdb=" CA GLY F 171 " pdb=" C GLY F 171 " ideal model delta sigma weight residual 114.16 108.57 5.59 1.21e+00 6.83e-01 2.13e+01 angle pdb=" N ILE 6 51 " pdb=" CA ILE 6 51 " pdb=" C ILE 6 51 " ideal model delta sigma weight residual 107.89 112.48 -4.59 1.09e+00 8.42e-01 1.77e+01 angle pdb=" C ILE I 75 " pdb=" N LYS I 76 " pdb=" CA LYS I 76 " ideal model delta sigma weight residual 121.80 111.66 10.14 2.44e+00 1.68e-01 1.73e+01 ... (remaining 65268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 19496 17.81 - 35.61: 2903 35.61 - 53.42: 1483 53.42 - 71.22: 766 71.22 - 89.03: 192 Dihedral angle restraints: 24840 sinusoidal: 18261 harmonic: 6579 Sorted by residual: dihedral pdb=" C4' A 2 195 " pdb=" C3' A 2 195 " pdb=" C2' A 2 195 " pdb=" C1' A 2 195 " ideal model delta sinusoidal sigma weight residual 36.34 -42.21 78.55 1 3.10e+00 1.04e-01 8.01e+02 dihedral pdb=" C4' A 2 105 " pdb=" C3' A 2 105 " pdb=" C2' A 2 105 " pdb=" C1' A 2 105 " ideal model delta sinusoidal sigma weight residual 36.35 -41.15 77.49 1 3.10e+00 1.04e-01 7.83e+02 dihedral pdb=" C4' A 2 759 " pdb=" C3' A 2 759 " pdb=" C2' A 2 759 " pdb=" C1' A 2 759 " ideal model delta sinusoidal sigma weight residual 36.34 -40.20 76.55 1 3.10e+00 1.04e-01 7.67e+02 ... (remaining 24837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5804 0.083 - 0.167: 1033 0.167 - 0.250: 885 0.250 - 0.333: 317 0.333 - 0.417: 4 Chirality restraints: 8043 Sorted by residual: chirality pdb=" C3' A2M 2 373 " pdb=" C4' A2M 2 373 " pdb=" O3' A2M 2 373 " pdb=" C2' A2M 2 373 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" P U 2 462 " pdb=" OP1 U 2 462 " pdb=" OP2 U 2 462 " pdb=" O5' U 2 462 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" P G 2 533 " pdb=" OP1 G 2 533 " pdb=" OP2 G 2 533 " pdb=" O5' G 2 533 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 8040 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 59 " 0.044 2.00e-02 2.50e+03 1.97e-02 1.07e+01 pdb=" N9 A 2 59 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A 2 59 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 2 59 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 2 59 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 2 59 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A 2 59 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A 2 59 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A 2 59 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 59 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A 2 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 587 " 0.041 2.00e-02 2.50e+03 1.86e-02 9.52e+00 pdb=" N9 A 2 587 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A 2 587 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A 2 587 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A 2 587 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 2 587 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A 2 587 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A 2 587 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A 2 587 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A 2 587 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 587 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 197 " -0.022 2.00e-02 2.50e+03 2.33e-02 9.51e+00 pdb=" CG PHE F 197 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE F 197 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE F 197 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE F 197 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 197 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 197 " -0.003 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 113 2.45 - 3.06: 23543 3.06 - 3.67: 62698 3.67 - 4.29: 105228 4.29 - 4.90: 156245 Nonbonded interactions: 347827 Sorted by model distance: nonbonded pdb=" OP2 G 2 727 " pdb="MG MG 21608 " model vdw 1.835 2.170 nonbonded pdb=" OP2 G 2 113 " pdb="MG MG 21622 " model vdw 1.960 2.170 nonbonded pdb=" OP1 A 2 587 " pdb="MG MG 21606 " model vdw 2.003 2.170 nonbonded pdb=" OP1 G 21474 " pdb="MG MG 21609 " model vdw 2.030 2.170 nonbonded pdb=" O TYR A 23 " pdb=" OG1 THR A 81 " model vdw 2.069 3.040 ... (remaining 347822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.820 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 47.520 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.013 0.843 44595 Z= 0.703 Angle : 1.343 65.502 65297 Z= 0.551 Chirality : 0.105 0.417 8043 Planarity : 0.007 0.062 4311 Dihedral : 21.405 89.030 20616 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.62 % Favored : 89.29 % Rotamer: Outliers : 1.12 % Allowed : 11.79 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.14), residues: 2259 helix: -3.45 (0.16), residues: 516 sheet: -2.65 (0.22), residues: 460 loop : -3.37 (0.14), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 179 TYR 0.026 0.003 TYR I 130 PHE 0.054 0.004 PHE F 197 TRP 0.030 0.003 TRP 6 60 HIS 0.015 0.003 HIS I 13 Details of bonding type rmsd/Z covalent geometry : bond 0.01228 / 0.57 (44574) covalent geometry : angle 1.22906 / 0.54 (65273) hydrogen bonds : bond 0.19245 / 9.75 ( 1222) hydrogen bonds : angle 6.22593 / 2.45 ( 2663) metal coordination : bond 0.11861 / 5.98 ( 20) metal coordination : angle 28.32573 / 12.12 ( 24) Misc. bond : bond 0.84315 / 42.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 390 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 ASP cc_start: 0.7571 (p0) cc_final: 0.7366 (p0) REVERT: E 224 ASP cc_start: 0.6292 (p0) cc_final: 0.6078 (p0) REVERT: N 76 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: W 22 ASP cc_start: 0.7085 (p0) cc_final: 0.6872 (p0) outliers start: 22 outliers final: 8 residues processed: 406 average time/residue: 0.2642 time to fit residues: 173.4022 Evaluate side-chains 306 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 297 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain N residue 76 GLN Chi-restraints excluded: chain 6 residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN B 65 GLN D 176 GLN E 99 HIS F 35 HIS I 9 ASN J 121 ASN M 80 HIS N 66 ASN N 130 ASN Q 85 HIS Q 112 HIS W 27 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.048368 restraints weight = 153420.724| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.59 r_work: 0.2613 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44595 Z= 0.179 Angle : 1.267 28.203 65297 Z= 0.505 Chirality : 0.104 1.449 8043 Planarity : 0.005 0.049 4311 Dihedral : 19.711 169.771 15732 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.58 % Allowed : 15.50 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.16), residues: 2259 helix: -1.95 (0.21), residues: 508 sheet: -1.94 (0.23), residues: 466 loop : -2.70 (0.15), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 8 TYR 0.016 0.001 TYR Q 148 PHE 0.012 0.001 PHE F 197 TRP 0.008 0.001 TRP 0 18 HIS 0.005 0.001 HIS Q 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (44574) covalent geometry : angle 1.24910 / 0.50 (65273) hydrogen bonds : bond 0.05383 / 2.74 ( 1222) hydrogen bonds : angle 4.04613 / 1.63 ( 2663) metal coordination : bond 0.01468 / 0.74 ( 20) metal coordination : angle 11.21741 / 5.09 ( 24) Misc. bond : bond 0.00395 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8316 (pm20) cc_final: 0.8076 (pm20) REVERT: B 197 MET cc_start: 0.8259 (tmm) cc_final: 0.7531 (tmm) REVERT: E 132 MET cc_start: 0.8853 (mtp) cc_final: 0.8490 (mtp) REVERT: E 217 ASP cc_start: 0.8926 (p0) cc_final: 0.8726 (p0) REVERT: E 224 ASP cc_start: 0.8640 (p0) cc_final: 0.8206 (p0) REVERT: F 14 ASP cc_start: 0.8899 (p0) cc_final: 0.8682 (p0) REVERT: F 30 GLN cc_start: 0.8720 (mt0) cc_final: 0.8438 (mt0) REVERT: G 37 GLN cc_start: 0.9085 (mm110) cc_final: 0.8813 (mm-40) REVERT: G 113 SER cc_start: 0.9337 (t) cc_final: 0.9114 (t) REVERT: I 64 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8629 (pt0) REVERT: I 90 GLU cc_start: 0.8946 (tt0) cc_final: 0.8624 (tt0) REVERT: I 115 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9059 (tt0) REVERT: J 40 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8701 (mm-40) REVERT: J 48 THR cc_start: 0.9302 (p) cc_final: 0.8745 (t) REVERT: J 67 ASP cc_start: 0.8853 (t0) cc_final: 0.8582 (t70) REVERT: J 104 GLU cc_start: 0.8024 (pm20) cc_final: 0.7534 (pm20) REVERT: N 61 GLU cc_start: 0.8612 (tp30) cc_final: 0.8049 (tp30) REVERT: N 64 GLN cc_start: 0.8887 (tp40) cc_final: 0.8579 (mt0) REVERT: Q 43 GLU cc_start: 0.9029 (mp0) cc_final: 0.8734 (mp0) REVERT: Q 149 ASP cc_start: 0.8490 (p0) cc_final: 0.7384 (p0) REVERT: Q 151 GLU cc_start: 0.8207 (pm20) cc_final: 0.7335 (pm20) REVERT: R 42 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9192 (mmmm) REVERT: W 48 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8606 (mt-10) REVERT: W 62 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8352 (pt0) REVERT: 0 1 MET cc_start: 0.8408 (ttt) cc_final: 0.8191 (ttt) outliers start: 31 outliers final: 16 residues processed: 379 average time/residue: 0.2354 time to fit residues: 149.0949 Evaluate side-chains 331 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 314 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain 6 residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [154, 291, 319, 244, 295, 318, 303, 49, 311, 110, 195] chunk 154 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 319 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 311 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 195 optimal weight: 30.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 GLN B 178 ASN E 192 ASN F 203 ASN J 116 GLN Q 35 ASN R 10 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.044801 restraints weight = 163495.417| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.72 r_work: 0.2516 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 44595 Z= 0.293 Angle : 1.085 19.149 65297 Z= 0.444 Chirality : 0.089 1.231 8043 Planarity : 0.005 0.057 4311 Dihedral : 19.743 174.882 15724 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.20 % Allowed : 16.16 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.16), residues: 2259 helix: -1.22 (0.22), residues: 513 sheet: -1.57 (0.23), residues: 468 loop : -2.32 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 126 TYR 0.012 0.001 TYR I 46 PHE 0.020 0.001 PHE F 197 TRP 0.026 0.001 TRP A 19 HIS 0.005 0.001 HIS F 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.29 (44574) covalent geometry : angle 1.07341 / 0.44 (65273) hydrogen bonds : bond 0.06239 / 3.18 ( 1222) hydrogen bonds : angle 3.86337 / 1.56 ( 2663) metal coordination : bond 0.01295 / 0.68 ( 20) metal coordination : angle 8.48229 / 3.78 ( 24) Misc. bond : bond 0.00324 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 324 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8610 (pm20) cc_final: 0.8356 (pm20) REVERT: B 197 MET cc_start: 0.8553 (tmm) cc_final: 0.7607 (tmm) REVERT: E 132 MET cc_start: 0.8928 (mtp) cc_final: 0.8464 (mtp) REVERT: E 224 ASP cc_start: 0.8741 (p0) cc_final: 0.8273 (p0) REVERT: F 30 GLN cc_start: 0.8891 (mt0) cc_final: 0.8624 (mt0) REVERT: F 33 ASP cc_start: 0.8932 (t0) cc_final: 0.8582 (t0) REVERT: G 113 SER cc_start: 0.9276 (t) cc_final: 0.9053 (t) REVERT: J 48 THR cc_start: 0.9304 (p) cc_final: 0.8850 (t) REVERT: J 67 ASP cc_start: 0.9011 (t0) cc_final: 0.8770 (t70) REVERT: N 61 GLU cc_start: 0.8738 (tp30) cc_final: 0.8487 (tp30) REVERT: N 69 MET cc_start: 0.9150 (mmm) cc_final: 0.8852 (mmm) REVERT: N 99 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8093 (mt-10) REVERT: N 116 MET cc_start: 0.9358 (ppp) cc_final: 0.9098 (ppp) REVERT: Q 43 GLU cc_start: 0.9011 (mp0) cc_final: 0.8751 (mp0) REVERT: Q 96 MET cc_start: 0.9277 (tpp) cc_final: 0.9073 (tmm) REVERT: Q 149 ASP cc_start: 0.8002 (p0) cc_final: 0.7625 (p0) REVERT: Q 151 GLU cc_start: 0.8363 (pm20) cc_final: 0.7972 (pm20) REVERT: R 94 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9034 (mm) REVERT: V 47 ASN cc_start: 0.9229 (t0) cc_final: 0.8907 (t0) REVERT: W 57 ARG cc_start: 0.8964 (ttm-80) cc_final: 0.8640 (mtp-110) REVERT: W 62 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8583 (mp0) outliers start: 63 outliers final: 39 residues processed: 360 average time/residue: 0.2375 time to fit residues: 143.3230 Evaluate side-chains 348 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [155, 124, 314, 197, 249, 220, 131, 130, 179, 293, 208] chunk 155 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 314 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.063265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.046221 restraints weight = 161922.613| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.72 r_work: 0.2568 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44595 Z= 0.194 Angle : 0.983 17.156 65297 Z= 0.401 Chirality : 0.081 1.162 8043 Planarity : 0.005 0.057 4311 Dihedral : 19.542 178.010 15724 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.59 % Allowed : 17.12 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.17), residues: 2259 helix: -0.70 (0.23), residues: 511 sheet: -1.28 (0.24), residues: 461 loop : -2.00 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 16 TYR 0.011 0.001 TYR J 62 PHE 0.012 0.001 PHE E 186 TRP 0.007 0.001 TRP A 19 HIS 0.004 0.001 HIS W 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (44574) covalent geometry : angle 0.97423 / 0.40 (65273) hydrogen bonds : bond 0.05487 / 2.80 ( 1222) hydrogen bonds : angle 3.58206 / 1.45 ( 2663) metal coordination : bond 0.00876 / 0.46 ( 20) metal coordination : angle 7.04290 / 3.14 ( 24) Misc. bond : bond 0.00086 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 331 time to evaluate : 1.004 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: A 103 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8907 (ptm-80) REVERT: A 185 GLU cc_start: 0.8688 (pm20) cc_final: 0.8428 (pm20) REVERT: B 197 MET cc_start: 0.8738 (tmm) cc_final: 0.7696 (tmm) REVERT: C 11 ILE cc_start: 0.9451 (mp) cc_final: 0.9233 (mp) REVERT: E 132 MET cc_start: 0.8895 (mtp) cc_final: 0.8385 (mtp) REVERT: E 224 ASP cc_start: 0.8702 (p0) cc_final: 0.8240 (p0) REVERT: F 30 GLN cc_start: 0.8907 (mt0) cc_final: 0.8666 (mt0) REVERT: F 33 ASP cc_start: 0.8843 (t0) cc_final: 0.8595 (t0) REVERT: G 113 SER cc_start: 0.9168 (t) cc_final: 0.8913 (t) REVERT: J 31 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8975 (mm-30) REVERT: J 48 THR cc_start: 0.9353 (p) cc_final: 0.8889 (t) REVERT: N 61 GLU cc_start: 0.8758 (tp30) cc_final: 0.8472 (tp30) REVERT: N 64 GLN cc_start: 0.9077 (tp40) cc_final: 0.8658 (mt0) REVERT: Q 43 GLU cc_start: 0.9089 (mp0) cc_final: 0.8870 (mp0) REVERT: R 94 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.8959 (mm) REVERT: V 2 GLU cc_start: 0.8951 (tp30) cc_final: 0.8520 (tp30) REVERT: V 47 ASN cc_start: 0.9247 (t0) cc_final: 0.8944 (t0) REVERT: V 82 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8764 (mm-30) REVERT: W 19 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8954 (tptt) REVERT: 6 37 MET cc_start: 0.5672 (mpp) cc_final: 0.5411 (mpp) outliers start: 51 outliers final: 31 residues processed: 364 average time/residue: 0.2304 time to fit residues: 142.0348 Evaluate side-chains 341 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [181, 242, 316, 194, 54, 18, 189, 294, 97, 117, 22] chunk 181 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 294 optimal weight: 0.2980 chunk 97 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.045071 restraints weight = 162404.060| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.72 r_work: 0.2532 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 44595 Z= 0.251 Angle : 1.013 17.212 65297 Z= 0.415 Chirality : 0.082 1.086 8043 Planarity : 0.005 0.056 4311 Dihedral : 19.596 177.650 15724 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.30 % Allowed : 17.73 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.17), residues: 2259 helix: -0.35 (0.23), residues: 512 sheet: -1.13 (0.24), residues: 463 loop : -1.83 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 57 TYR 0.018 0.001 TYR B 177 PHE 0.014 0.001 PHE E 186 TRP 0.006 0.001 TRP 0 18 HIS 0.003 0.001 HIS F 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (44574) covalent geometry : angle 1.00529 / 0.41 (65273) hydrogen bonds : bond 0.05930 / 3.03 ( 1222) hydrogen bonds : angle 3.62093 / 1.47 ( 2663) metal coordination : bond 0.01086 / 0.56 ( 20) metal coordination : angle 6.54650 / 2.89 ( 24) Misc. bond : bond 0.00134 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 1.007 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: A 103 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8924 (ptm-80) REVERT: A 185 GLU cc_start: 0.8739 (pm20) cc_final: 0.8524 (pm20) REVERT: B 28 MET cc_start: 0.9151 (mmm) cc_final: 0.8640 (mmm) REVERT: B 75 TYR cc_start: 0.9485 (m-80) cc_final: 0.9247 (m-80) REVERT: B 197 MET cc_start: 0.8832 (tmm) cc_final: 0.7980 (tmm) REVERT: C 11 ILE cc_start: 0.9453 (mp) cc_final: 0.9224 (mp) REVERT: C 57 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8911 (pttt) REVERT: E 132 MET cc_start: 0.8926 (mtp) cc_final: 0.8369 (mtp) REVERT: E 224 ASP cc_start: 0.8669 (p0) cc_final: 0.8179 (p0) REVERT: F 33 ASP cc_start: 0.8901 (t0) cc_final: 0.8612 (t0) REVERT: G 113 SER cc_start: 0.9162 (t) cc_final: 0.8913 (t) REVERT: J 48 THR cc_start: 0.9352 (p) cc_final: 0.8906 (t) REVERT: J 102 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8524 (pp20) REVERT: M 37 GLU cc_start: 0.8322 (mp0) cc_final: 0.7761 (mp0) REVERT: N 61 GLU cc_start: 0.8805 (tp30) cc_final: 0.8491 (tp30) REVERT: N 64 GLN cc_start: 0.9084 (tp40) cc_final: 0.8641 (mt0) REVERT: N 116 MET cc_start: 0.9353 (ppp) cc_final: 0.9152 (ppp) REVERT: Q 43 GLU cc_start: 0.9110 (mp0) cc_final: 0.8900 (mp0) REVERT: R 94 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9011 (mm) REVERT: V 1 MET cc_start: 0.8987 (ppp) cc_final: 0.8071 (ppp) REVERT: V 18 GLU cc_start: 0.8563 (mp0) cc_final: 0.8350 (mp0) REVERT: V 49 GLU cc_start: 0.8746 (pm20) cc_final: 0.8488 (pm20) REVERT: W 62 GLU cc_start: 0.8615 (mp0) cc_final: 0.8353 (pm20) REVERT: 6 37 MET cc_start: 0.6054 (mpp) cc_final: 0.5768 (mpp) outliers start: 65 outliers final: 48 residues processed: 354 average time/residue: 0.2268 time to fit residues: 136.5000 Evaluate side-chains 356 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [10, 95, 215, 217, 281, 248, 237, 163, 159, 6, 97] chunk 10 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 281 optimal weight: 0.3980 chunk 248 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 HIS Q 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.061993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044930 restraints weight = 163410.497| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.71 r_work: 0.2530 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44595 Z= 0.259 Angle : 1.012 17.324 65297 Z= 0.414 Chirality : 0.082 1.075 8043 Planarity : 0.005 0.059 4311 Dihedral : 19.626 178.587 15724 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.76 % Allowed : 18.09 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.17), residues: 2259 helix: -0.10 (0.23), residues: 512 sheet: -1.04 (0.24), residues: 465 loop : -1.71 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 60 TYR 0.016 0.001 TYR B 177 PHE 0.014 0.001 PHE E 186 TRP 0.006 0.001 TRP 0 18 HIS 0.004 0.001 HIS W 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.26 (44574) covalent geometry : angle 1.00528 / 0.41 (65273) hydrogen bonds : bond 0.05941 / 3.03 ( 1222) hydrogen bonds : angle 3.61763 / 1.46 ( 2663) metal coordination : bond 0.01052 / 0.55 ( 20) metal coordination : angle 6.22765 / 2.75 ( 24) Misc. bond : bond 0.00135 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 311 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8967 (ptm-80) REVERT: B 75 TYR cc_start: 0.9501 (m-80) cc_final: 0.9285 (m-80) REVERT: B 197 MET cc_start: 0.8848 (tmm) cc_final: 0.8215 (tmm) REVERT: C 11 ILE cc_start: 0.9383 (mp) cc_final: 0.9168 (mp) REVERT: C 57 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8868 (ptpt) REVERT: D 76 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8695 (ttt90) REVERT: E 132 MET cc_start: 0.8898 (mtp) cc_final: 0.8306 (mtp) REVERT: E 224 ASP cc_start: 0.8662 (p0) cc_final: 0.8143 (p0) REVERT: F 30 GLN cc_start: 0.8763 (mt0) cc_final: 0.8562 (mt0) REVERT: F 33 ASP cc_start: 0.8918 (t0) cc_final: 0.8605 (t0) REVERT: G 113 SER cc_start: 0.9102 (t) cc_final: 0.8845 (t) REVERT: J 48 THR cc_start: 0.9382 (p) cc_final: 0.8970 (t) REVERT: J 102 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8398 (pp20) REVERT: M 37 GLU cc_start: 0.8232 (mp0) cc_final: 0.7920 (mp0) REVERT: N 64 GLN cc_start: 0.9092 (tp40) cc_final: 0.8731 (tt0) REVERT: N 116 MET cc_start: 0.9384 (ppp) cc_final: 0.9117 (ppp) REVERT: Q 93 GLU cc_start: 0.8297 (mm-30) cc_final: 0.6475 (mm-30) REVERT: Q 96 MET cc_start: 0.9156 (tmm) cc_final: 0.8825 (ptt) REVERT: Q 151 GLU cc_start: 0.8361 (pm20) cc_final: 0.8032 (pm20) REVERT: R 94 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9006 (mm) REVERT: V 1 MET cc_start: 0.8959 (ppp) cc_final: 0.8166 (ppp) REVERT: V 2 GLU cc_start: 0.8898 (tp30) cc_final: 0.8404 (tp30) REVERT: V 18 GLU cc_start: 0.8581 (mp0) cc_final: 0.8362 (mp0) REVERT: W 57 ARG cc_start: 0.8627 (mtp-110) cc_final: 0.8248 (mtp-110) REVERT: 6 37 MET cc_start: 0.6148 (mpp) cc_final: 0.5914 (mpp) outliers start: 74 outliers final: 49 residues processed: 360 average time/residue: 0.2314 time to fit residues: 140.4917 Evaluate side-chains 353 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [70, 259, 232, 158, 118, 15, 83, 40, 42, 219, 297] chunk 70 optimal weight: 7.9990 chunk 259 optimal weight: 0.8980 chunk 232 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 297 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.045539 restraints weight = 161507.066| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.69 r_work: 0.2556 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 44595 Z= 0.216 Angle : 0.981 17.143 65297 Z= 0.402 Chirality : 0.079 1.024 8043 Planarity : 0.005 0.061 4311 Dihedral : 19.576 179.612 15724 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.25 % Allowed : 19.05 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2259 helix: 0.16 (0.24), residues: 506 sheet: -0.91 (0.24), residues: 465 loop : -1.58 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 17 TYR 0.017 0.001 TYR B 177 PHE 0.014 0.001 PHE E 186 TRP 0.006 0.001 TRP 0 18 HIS 0.003 0.001 HIS Q 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (44574) covalent geometry : angle 0.97521 / 0.40 (65273) hydrogen bonds : bond 0.05645 / 2.88 ( 1222) hydrogen bonds : angle 3.53238 / 1.43 ( 2663) metal coordination : bond 0.00927 / 0.48 ( 20) metal coordination : angle 5.67071 / 2.50 ( 24) Misc. bond : bond 0.00105 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8998 (ptm-80) REVERT: A 185 GLU cc_start: 0.8488 (pm20) cc_final: 0.8280 (pm20) REVERT: B 197 MET cc_start: 0.8856 (tmm) cc_final: 0.8362 (tmm) REVERT: C 11 ILE cc_start: 0.9368 (mp) cc_final: 0.9134 (mp) REVERT: C 57 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8960 (ptpt) REVERT: D 76 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8626 (ttt90) REVERT: E 224 ASP cc_start: 0.8598 (p0) cc_final: 0.8069 (p0) REVERT: F 30 GLN cc_start: 0.8791 (mt0) cc_final: 0.8591 (mt0) REVERT: F 33 ASP cc_start: 0.8894 (t0) cc_final: 0.8569 (t0) REVERT: G 113 SER cc_start: 0.9085 (t) cc_final: 0.8825 (t) REVERT: J 48 THR cc_start: 0.9354 (p) cc_final: 0.8933 (t) REVERT: J 102 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8377 (pp20) REVERT: M 37 GLU cc_start: 0.8289 (mp0) cc_final: 0.7980 (mp0) REVERT: N 64 GLN cc_start: 0.9078 (tp40) cc_final: 0.8727 (tt0) REVERT: N 116 MET cc_start: 0.9359 (ppp) cc_final: 0.9155 (ppp) REVERT: Q 43 GLU cc_start: 0.9051 (mp0) cc_final: 0.8762 (mp0) REVERT: Q 93 GLU cc_start: 0.8287 (mm-30) cc_final: 0.6263 (mm-30) REVERT: Q 96 MET cc_start: 0.9202 (tmm) cc_final: 0.8745 (ptt) REVERT: Q 149 ASP cc_start: 0.7798 (p0) cc_final: 0.7596 (p0) REVERT: R 94 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8995 (mm) REVERT: V 1 MET cc_start: 0.9007 (ppp) cc_final: 0.8266 (ppp) REVERT: V 2 GLU cc_start: 0.8851 (tp30) cc_final: 0.8409 (tp30) REVERT: V 18 GLU cc_start: 0.8577 (mp0) cc_final: 0.8365 (mp0) REVERT: W 57 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.8278 (mtp-110) REVERT: W 62 GLU cc_start: 0.8925 (pm20) cc_final: 0.8659 (pm20) REVERT: 6 37 MET cc_start: 0.6112 (mpp) cc_final: 0.5880 (mpp) outliers start: 64 outliers final: 48 residues processed: 350 average time/residue: 0.2300 time to fit residues: 136.1367 Evaluate side-chains 354 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 16 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [67, 256, 1, 71, 298, 85, 217, 308, 226, 218, 160] chunk 67 optimal weight: 7.9990 chunk 256 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.062862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.045992 restraints weight = 161375.664| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.65 r_work: 0.2570 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 44595 Z= 0.195 Angle : 0.965 16.918 65297 Z= 0.396 Chirality : 0.078 0.983 8043 Planarity : 0.005 0.061 4311 Dihedral : 19.542 179.174 15724 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.10 % Allowed : 19.66 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2259 helix: 0.27 (0.24), residues: 508 sheet: -0.82 (0.24), residues: 460 loop : -1.52 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 33 TYR 0.017 0.001 TYR B 177 PHE 0.013 0.001 PHE E 186 TRP 0.006 0.001 TRP 0 18 HIS 0.003 0.001 HIS Q 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (44574) covalent geometry : angle 0.96018 / 0.40 (65273) hydrogen bonds : bond 0.05517 / 2.82 ( 1222) hydrogen bonds : angle 3.49803 / 1.41 ( 2663) metal coordination : bond 0.00872 / 0.45 ( 20) metal coordination : angle 5.35929 / 2.38 ( 24) Misc. bond : bond 0.00100 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8939 (ptm-80) REVERT: A 185 GLU cc_start: 0.8570 (pm20) cc_final: 0.8336 (pm20) REVERT: B 197 MET cc_start: 0.8893 (tmm) cc_final: 0.8426 (tmm) REVERT: C 11 ILE cc_start: 0.9364 (mp) cc_final: 0.9134 (mp) REVERT: D 76 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8643 (ttt90) REVERT: E 224 ASP cc_start: 0.8576 (p0) cc_final: 0.8042 (p0) REVERT: F 30 GLN cc_start: 0.8795 (mt0) cc_final: 0.8595 (mt0) REVERT: F 33 ASP cc_start: 0.8862 (t0) cc_final: 0.8526 (t0) REVERT: G 113 SER cc_start: 0.9041 (t) cc_final: 0.8788 (t) REVERT: M 37 GLU cc_start: 0.8279 (mp0) cc_final: 0.7938 (mp0) REVERT: N 64 GLN cc_start: 0.9071 (tp40) cc_final: 0.8725 (tt0) REVERT: Q 43 GLU cc_start: 0.9024 (mp0) cc_final: 0.8739 (mp0) REVERT: R 50 GLU cc_start: 0.9223 (tt0) cc_final: 0.8951 (tt0) REVERT: R 94 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8999 (mm) REVERT: V 1 MET cc_start: 0.9013 (ppp) cc_final: 0.8350 (ppp) REVERT: V 2 GLU cc_start: 0.8863 (tp30) cc_final: 0.8661 (tp30) REVERT: V 18 GLU cc_start: 0.8564 (mp0) cc_final: 0.8323 (mp0) REVERT: W 57 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8252 (mtp-110) REVERT: W 62 GLU cc_start: 0.8897 (pm20) cc_final: 0.8593 (pm20) REVERT: 6 37 MET cc_start: 0.6163 (mpp) cc_final: 0.5930 (mpp) outliers start: 61 outliers final: 47 residues processed: 350 average time/residue: 0.2410 time to fit residues: 142.9746 Evaluate side-chains 354 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 304 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 16 CYS Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [90, 279, 300, 126, 72, 243, 3, 179, 190, 227, 162] chunk 90 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 HIS Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.061351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.044252 restraints weight = 162731.055| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.73 r_work: 0.2509 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 44595 Z= 0.293 Angle : 1.047 17.474 65297 Z= 0.430 Chirality : 0.083 1.100 8043 Planarity : 0.005 0.064 4311 Dihedral : 19.666 179.605 15724 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.30 % Allowed : 19.87 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2259 helix: 0.08 (0.23), residues: 532 sheet: -0.86 (0.24), residues: 461 loop : -1.54 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 126 TYR 0.017 0.001 TYR B 177 PHE 0.017 0.001 PHE I 97 TRP 0.007 0.001 TRP I 89 HIS 0.003 0.001 HIS F 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.29 (44574) covalent geometry : angle 1.04090 / 0.43 (65273) hydrogen bonds : bond 0.06191 / 3.16 ( 1222) hydrogen bonds : angle 3.67060 / 1.49 ( 2663) metal coordination : bond 0.01296 / 0.67 ( 20) metal coordination : angle 5.80756 / 2.52 ( 24) Misc. bond : bond 0.00158 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8984 (ptm-80) REVERT: B 197 MET cc_start: 0.8930 (tmm) cc_final: 0.8463 (tmm) REVERT: C 11 ILE cc_start: 0.9373 (mp) cc_final: 0.9150 (mp) REVERT: C 57 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8888 (pttt) REVERT: C 61 GLU cc_start: 0.9074 (pm20) cc_final: 0.8718 (pm20) REVERT: D 76 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8728 (ttt90) REVERT: E 168 VAL cc_start: 0.9108 (t) cc_final: 0.8900 (t) REVERT: E 207 MET cc_start: 0.9012 (tpp) cc_final: 0.8107 (tpp) REVERT: E 224 ASP cc_start: 0.8653 (p0) cc_final: 0.8112 (p0) REVERT: F 30 GLN cc_start: 0.8920 (mt0) cc_final: 0.8702 (mt0) REVERT: F 33 ASP cc_start: 0.8975 (t0) cc_final: 0.8664 (t0) REVERT: G 77 ASP cc_start: 0.8329 (m-30) cc_final: 0.8019 (t0) REVERT: G 113 SER cc_start: 0.9063 (t) cc_final: 0.8799 (t) REVERT: J 48 THR cc_start: 0.9353 (p) cc_final: 0.8966 (t) REVERT: J 102 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8538 (pp20) REVERT: M 37 GLU cc_start: 0.8317 (mp0) cc_final: 0.7959 (mp0) REVERT: N 98 ASP cc_start: 0.9044 (m-30) cc_final: 0.8555 (m-30) REVERT: N 101 ASP cc_start: 0.8802 (m-30) cc_final: 0.8283 (m-30) REVERT: Q 43 GLU cc_start: 0.9061 (mp0) cc_final: 0.8794 (mp0) REVERT: R 94 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9057 (mm) REVERT: V 1 MET cc_start: 0.9185 (ppp) cc_final: 0.8531 (ppp) REVERT: V 2 GLU cc_start: 0.8928 (tp30) cc_final: 0.8701 (tp30) REVERT: V 18 GLU cc_start: 0.8616 (mp0) cc_final: 0.8386 (mp0) REVERT: V 90 ASP cc_start: 0.8908 (t0) cc_final: 0.8666 (t0) REVERT: W 57 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8363 (mtp-110) REVERT: W 62 GLU cc_start: 0.8869 (pm20) cc_final: 0.8489 (pm20) REVERT: 6 96 ARG cc_start: 0.6848 (ttm170) cc_final: 0.6503 (pmt-80) outliers start: 65 outliers final: 55 residues processed: 348 average time/residue: 0.2363 time to fit residues: 138.4772 Evaluate side-chains 352 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 16 CYS Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [39, 309, 170, 33, 210, 137, 134, 99, 64, 112, 144] chunk 39 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 137 optimal weight: 0.2980 chunk 134 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.045113 restraints weight = 161561.608| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.68 r_work: 0.2537 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 44595 Z= 0.223 Angle : 1.003 17.299 65297 Z= 0.414 Chirality : 0.080 1.052 8043 Planarity : 0.005 0.068 4311 Dihedral : 19.633 179.745 15724 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.79 % Allowed : 20.53 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2259 helix: 0.18 (0.23), residues: 527 sheet: -0.79 (0.24), residues: 461 loop : -1.51 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG 6 85 TYR 0.017 0.001 TYR B 177 PHE 0.014 0.001 PHE E 186 TRP 0.007 0.001 TRP I 89 HIS 0.004 0.001 HIS W 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (44574) covalent geometry : angle 0.99817 / 0.41 (65273) hydrogen bonds : bond 0.05732 / 2.93 ( 1222) hydrogen bonds : angle 3.59426 / 1.45 ( 2663) metal coordination : bond 0.00990 / 0.51 ( 20) metal coordination : angle 5.33004 / 2.31 ( 24) Misc. bond : bond 0.00116 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8939 (ptm-80) REVERT: B 197 MET cc_start: 0.8899 (tmm) cc_final: 0.8423 (tmm) REVERT: C 11 ILE cc_start: 0.9357 (mp) cc_final: 0.9121 (mp) REVERT: C 57 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8870 (pttt) REVERT: C 61 GLU cc_start: 0.9046 (pm20) cc_final: 0.8674 (pm20) REVERT: D 76 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8731 (ttt90) REVERT: E 168 VAL cc_start: 0.9096 (t) cc_final: 0.8888 (t) REVERT: E 207 MET cc_start: 0.8997 (tpp) cc_final: 0.8136 (tpp) REVERT: E 224 ASP cc_start: 0.8645 (p0) cc_final: 0.8105 (p0) REVERT: F 30 GLN cc_start: 0.8929 (mt0) cc_final: 0.8712 (mt0) REVERT: F 33 ASP cc_start: 0.8941 (t0) cc_final: 0.8609 (t0) REVERT: G 77 ASP cc_start: 0.8306 (m-30) cc_final: 0.8000 (t0) REVERT: G 113 SER cc_start: 0.9044 (t) cc_final: 0.8787 (t) REVERT: J 48 THR cc_start: 0.9371 (p) cc_final: 0.8975 (t) REVERT: J 102 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8517 (pp20) REVERT: M 37 GLU cc_start: 0.8313 (mp0) cc_final: 0.7949 (mp0) REVERT: M 54 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8621 (mm-30) REVERT: N 64 GLN cc_start: 0.9090 (tp40) cc_final: 0.8802 (tt0) REVERT: N 98 ASP cc_start: 0.9035 (m-30) cc_final: 0.8559 (m-30) REVERT: N 101 ASP cc_start: 0.8804 (m-30) cc_final: 0.8298 (m-30) REVERT: Q 43 GLU cc_start: 0.9049 (mp0) cc_final: 0.8760 (mp0) REVERT: R 94 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9044 (mm) REVERT: V 1 MET cc_start: 0.9176 (ppp) cc_final: 0.8586 (ppp) REVERT: V 2 GLU cc_start: 0.8888 (tp30) cc_final: 0.8670 (tp30) REVERT: V 18 GLU cc_start: 0.8600 (mp0) cc_final: 0.8369 (mp0) REVERT: V 90 ASP cc_start: 0.8894 (t0) cc_final: 0.8650 (t0) REVERT: W 57 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8355 (mtp-110) REVERT: W 62 GLU cc_start: 0.8878 (pm20) cc_final: 0.8497 (pm20) REVERT: 6 96 ARG cc_start: 0.6838 (ttm170) cc_final: 0.6499 (pmt-80) outliers start: 55 outliers final: 50 residues processed: 343 average time/residue: 0.2300 time to fit residues: 133.3171 Evaluate side-chains 352 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 16 CYS Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [46, 198, 281, 101, 276, 58, 69, 209, 214, 49, 313] chunk 46 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 276 optimal weight: 0.1980 chunk 58 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 214 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047330 restraints weight = 160925.356| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.64 r_work: 0.2617 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44595 Z= 0.139 Angle : 0.938 16.634 65297 Z= 0.387 Chirality : 0.074 0.903 8043 Planarity : 0.005 0.068 4311 Dihedral : 19.505 178.683 15724 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.93 % Allowed : 21.39 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2259 helix: 0.32 (0.23), residues: 526 sheet: -0.70 (0.24), residues: 468 loop : -1.40 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 33 TYR 0.016 0.001 TYR B 177 PHE 0.011 0.001 PHE I 52 TRP 0.010 0.001 TRP C 41 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (44574) covalent geometry : angle 0.93353 / 0.39 (65273) hydrogen bonds : bond 0.05119 / 2.61 ( 1222) hydrogen bonds : angle 3.39861 / 1.37 ( 2663) metal coordination : bond 0.00756 / 0.38 ( 20) metal coordination : angle 4.91152 / 2.11 ( 24) Misc. bond : bond 0.00082 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10530.59 seconds wall clock time: 180 minutes 21.94 seconds (10821.94 seconds total)