Starting phenix.real_space_refine on Mon Oct 26 22:19:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.cif Found real_map, /net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6swe_10324/10_2026/6swe_10324.cif" } resolution = 3.1 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= 0.001 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 1 6.06 5 P 486 5.49 5 Mg 8 5.21 5 S 49 5.16 5 C 12428 2.51 5 N 4238 2.21 5 O 5527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s 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: 22737 Number of models: 1 Model: "" Number of chains: 21 Chain: "2" Number of atoms: 10068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 10068 Classifications: {'RNA': 10, 'RNAv2': 458} Modifications used: {'rna2p_pur': 41, 'rna2p_pyr': 37, 'rna3p': 10, 'rna3p_pur': 217, 'rna3p_pyr': 163} Link IDs: {'rna2p': 78, 'rna3p': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1720 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "K" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 817 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "O" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1151 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "P" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "T" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1057 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1223 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 11, 'TRANS': 137} Chain: "X" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Y" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 408 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1550 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "3" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 114} Chain: "4" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 384 Classifications: {'RNA': 1, 'RNAv2': 17} Modifications used: {'rna3p': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" 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 14985 SG CYS P 21 92.396 72.031 80.842 1.00 28.23 S ATOM 15010 SG CYS P 24 90.937 70.637 84.552 1.00 33.25 S ATOM 15125 SG CYS P 39 90.941 69.183 80.674 1.00 27.52 S ATOM 15152 SG CYS P 42 89.326 71.758 83.719 1.00 29.16 S Time building chain proxies: 4.81, per 1000 atoms: 0.21 Number of scatterers: 22737 At special positions: 0 Unit cell: (175.49, 130.8, 127.53, 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 1 29.99 S 49 16.00 P 486 15.00 Mg 8 11.99 O 5527 8.00 N 4238 7.00 C 12428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 828.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 39 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 42 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 21 " Number of angles added : 6 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 16 sheets defined 38.8% alpha, 11.2% beta 117 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'H' and resid 4 through 9 Processing helix chain 'H' and resid 16 through 20 Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.891A pdb=" N ALA H 59 " --> pdb=" O PHE H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 96 through 115 removed outlier: 3.771A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.989A pdb=" N GLU H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN H 129 " --> pdb=" O TRP H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 170 Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.536A pdb=" N ALA H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 213 removed outlier: 3.720A pdb=" N ILE H 210 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'K' and resid 46 through 51 Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 74 through 90 removed outlier: 3.820A pdb=" N GLU K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR K 90 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 102 removed outlier: 3.714A pdb=" N LYS K 96 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS K 98 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR K 102 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 Processing helix chain 'L' and resid 13 through 30 removed outlier: 3.722A pdb=" N GLU L 17 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU L 18 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 84 through 87 removed outlier: 3.867A pdb=" N ARG L 87 " --> pdb=" O GLN L 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 84 through 87' Processing helix chain 'O' and resid 20 through 25 Processing helix chain 'O' and resid 32 through 44 removed outlier: 3.827A pdb=" N MET O 38 " --> pdb=" O ASN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 54 Processing helix chain 'O' and resid 55 through 68 removed outlier: 3.750A pdb=" N ASP O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 73 Processing helix chain 'O' and resid 94 through 112 removed outlier: 4.119A pdb=" N ASP O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA O 101 " --> pdb=" O LYS O 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE O 112 " --> pdb=" O ARG O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 123 removed outlier: 3.529A pdb=" N ARG O 119 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 19 removed outlier: 3.959A pdb=" N ARG P 19 " --> pdb=" O LYS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 44 removed outlier: 3.959A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 40 through 44' Processing helix chain 'P' and resid 46 through 51 removed outlier: 3.677A pdb=" N LEU P 50 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 16 removed outlier: 3.515A pdb=" N LYS S 10 " --> pdb=" O GLN S 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.615A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 59 removed outlier: 3.615A pdb=" N ARG S 49 " --> pdb=" O LYS S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 17 Processing helix chain 'T' and resid 29 through 38 Processing helix chain 'T' and resid 41 through 57 removed outlier: 3.964A pdb=" N LEU T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 107 removed outlier: 3.740A pdb=" N PHE T 106 " --> pdb=" O LEU T 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 20 removed outlier: 3.702A pdb=" N GLN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG U 19 " --> pdb=" O ARG U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 23 No H-bonds generated for 'chain 'U' and resid 21 through 23' Processing helix chain 'U' and resid 31 through 35 removed outlier: 3.736A pdb=" N PHE U 34 " --> pdb=" O TRP U 31 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL U 35 " --> pdb=" O ALA U 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 31 through 35' Processing helix chain 'U' and resid 49 through 64 removed outlier: 4.013A pdb=" N TYR U 53 " --> pdb=" O ASP U 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG U 61 " --> pdb=" O SER U 57 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU U 64 " --> pdb=" O ARG U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 77 removed outlier: 4.391A pdb=" N THR U 75 " --> pdb=" O GLU U 71 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR U 76 " --> pdb=" O ARG U 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR U 77 " --> pdb=" O LEU U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 109 Processing helix chain 'U' and resid 122 through 139 removed outlier: 3.969A pdb=" N GLU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 11 through 25 removed outlier: 3.658A pdb=" N MET Z 15 " --> pdb=" O ALA Z 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS Z 23 " --> pdb=" O GLU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 56 removed outlier: 4.018A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY Z 56 " --> pdb=" O GLY Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 72 removed outlier: 3.964A pdb=" N ARG Z 63 " --> pdb=" O GLY Z 59 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU Z 64 " --> pdb=" O ARG Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 90 Processing helix chain 'Z' and resid 91 through 106 removed outlier: 4.449A pdb=" N VAL Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY Z 106 " --> pdb=" O ALA Z 102 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 123 removed outlier: 4.109A pdb=" N ALA Z 113 " --> pdb=" O PHE Z 109 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR Z 114 " --> pdb=" O ARG Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 156 through 161 Processing helix chain '3' and resid 13 through 21 Processing helix chain '3' and resid 22 through 28 removed outlier: 3.549A pdb=" N ALA 3 26 " --> pdb=" O ALA 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 35 through 46 removed outlier: 4.337A pdb=" N THR 3 39 " --> pdb=" O GLY 3 35 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS 3 41 " --> pdb=" O ASN 3 37 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA 3 42 " --> pdb=" O GLU 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 71 removed outlier: 4.193A pdb=" N GLU 3 71 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) Processing helix chain '3' and resid 83 through 90 Processing helix chain '3' and resid 108 through 122 removed outlier: 4.206A pdb=" N MET 3 116 " --> pdb=" O GLU 3 112 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 59 removed outlier: 4.345A pdb=" N ARG 6 58 " --> pdb=" O LYS 6 54 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL 6 59 " --> pdb=" O LEU 6 55 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 54 through 59' Processing helix chain '6' and resid 87 through 92 removed outlier: 3.710A pdb=" N VAL 6 91 " --> pdb=" O THR 6 87 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP 6 92 " --> pdb=" O GLN 6 88 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 87 through 92' Processing helix chain '6' and resid 92 through 97 removed outlier: 4.193A pdb=" N ARG 6 96 " --> pdb=" O ASP 6 92 " (cutoff:3.500A) removed outlier: 4.452A 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 102 through 107 removed outlier: 3.754A pdb=" N THR 6 106 " --> pdb=" O GLN 6 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 135 through 137 removed outlier: 8.196A pdb=" N ALA H 149 " --> pdb=" O ASN X 44 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ARG X 46 " --> pdb=" O ALA H 149 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP H 151 " --> pdb=" O ARG X 46 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL X 24 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG X 17 " --> pdb=" O VAL X 24 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN X 26 " --> pdb=" O ILE X 15 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU X 13 " --> pdb=" O LYS X 28 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG X 30 " --> pdb=" O VAL X 11 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL X 11 " --> pdb=" O ARG X 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 4 through 9 removed outlier: 6.955A pdb=" N ARG K 27 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL K 66 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 34 through 40 removed outlier: 5.904A pdb=" N GLY L 36 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP L 74 " --> pdb=" O GLY L 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 40 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS L 70 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L 8 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 45 through 50 removed outlier: 3.592A pdb=" N THR L 49 " --> pdb=" O ASP L 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 7 through 9 Processing sheet with id=AA6, first strand: chain 'O' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.546A pdb=" N LEU P 38 " --> pdb=" O ILE P 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 64 through 65 removed outlier: 3.808A pdb=" N ILE T 81 " --> pdb=" O VAL T 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 79 through 81 removed outlier: 4.092A pdb=" N ARG U 89 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 111 through 114 removed outlier: 3.503A pdb=" N GLY U 118 " --> pdb=" O VAL U 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 33 through 38 Processing sheet with id=AB3, first strand: chain 'Z' and resid 144 through 147 removed outlier: 4.218A pdb=" N GLY Z 127 " --> pdb=" O MET Z 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 31 through 33 removed outlier: 4.104A pdb=" N LYS 3 31 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE 3 102 " --> pdb=" O LYS 3 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 53 through 54 removed outlier: 7.177A pdb=" N ILE 3 53 " --> pdb=" O VAL 3 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '6' and resid 24 through 26 Processing sheet with id=AB7, first strand: chain '6' and resid 28 through 33 removed outlier: 6.880A pdb=" N ASP 6 38 " --> pdb=" O GLU 6 29 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA 6 31 " --> pdb=" O TRP 6 36 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TRP 6 36 " --> pdb=" O ALA 6 31 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG 6 47 " --> pdb=" O VAL 6 39 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3377 1.32 - 1.44: 8677 1.44 - 1.57: 11049 1.57 - 1.69: 969 1.69 - 1.81: 84 Bond restraints: 24156 Sorted by residual: bond pdb=" C LYS H 194 " pdb=" N ASP H 195 " ideal model delta sigma weight residual 1.331 1.242 0.089 2.07e-02 2.33e+03 1.83e+01 bond pdb=" CA GLU U 71 " pdb=" C GLU U 71 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.34e-02 5.57e+03 1.45e+01 bond pdb=" C4 B8H 2 938 " pdb=" C5 B8H 2 938 " ideal model delta sigma weight residual 1.444 1.369 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 4AC 21193 " pdb=" C6 4AC 21193 " ideal model delta sigma weight residual 1.356 1.294 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" C4 OMC 4 33 " pdb=" C5 OMC 4 33 " ideal model delta sigma weight residual 1.428 1.376 0.052 2.00e-02 2.50e+03 6.81e+00 ... (remaining 24151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 32611 2.19 - 4.37: 1907 4.37 - 6.56: 332 6.56 - 8.74: 40 8.74 - 10.93: 4 Bond angle restraints: 34894 Sorted by residual: angle pdb=" N ILE 3 62 " pdb=" CA ILE 3 62 " pdb=" C ILE 3 62 " ideal model delta sigma weight residual 112.29 105.78 6.51 9.40e-01 1.13e+00 4.79e+01 angle pdb=" N VAL 6 83 " pdb=" CA VAL 6 83 " pdb=" C VAL 6 83 " ideal model delta sigma weight residual 113.71 109.37 4.34 9.50e-01 1.11e+00 2.09e+01 angle pdb=" C3' G 21155 " pdb=" O3' G 21155 " pdb=" P G 21156 " ideal model delta sigma weight residual 119.70 124.67 -4.97 1.20e+00 6.94e-01 1.71e+01 angle pdb=" N GLY Y 41 " pdb=" CA GLY Y 41 " pdb=" C GLY Y 41 " ideal model delta sigma weight residual 113.58 109.48 4.10 1.07e+00 8.73e-01 1.47e+01 angle pdb=" N PRO K 119 " pdb=" CA PRO K 119 " pdb=" C PRO K 119 " ideal model delta sigma weight residual 112.47 120.27 -7.80 2.06e+00 2.36e-01 1.43e+01 ... (remaining 34889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 12097 29.39 - 58.78: 1282 58.78 - 88.17: 258 88.17 - 117.56: 3 117.56 - 146.95: 1 Dihedral angle restraints: 13641 sinusoidal: 9283 harmonic: 4358 Sorted by residual: dihedral pdb=" C4' A 21337 " pdb=" C3' A 21337 " pdb=" C2' A 21337 " pdb=" C1' A 21337 " ideal model delta sinusoidal sigma weight residual 36.34 -42.94 79.29 1 3.10e+00 1.04e-01 8.13e+02 dihedral pdb=" C4' G 21018 " pdb=" C3' G 21018 " pdb=" C2' G 21018 " pdb=" C1' G 21018 " ideal model delta sinusoidal sigma weight residual 36.35 -41.52 77.87 1 3.10e+00 1.04e-01 7.89e+02 dihedral pdb=" C4' C 21296 " pdb=" C3' C 21296 " pdb=" C2' C 21296 " pdb=" C1' C 21296 " ideal model delta sinusoidal sigma weight residual 36.35 -40.56 76.91 1 3.10e+00 1.04e-01 7.73e+02 ... (remaining 13638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2953 0.073 - 0.145: 617 0.145 - 0.218: 317 0.218 - 0.291: 299 0.291 - 0.364: 50 Chirality restraints: 4236 Sorted by residual: chirality pdb=" C3' A 21337 " pdb=" C4' A 21337 " pdb=" O3' A 21337 " pdb=" C2' A 21337 " both_signs ideal model delta sigma weight residual False -2.50 -2.86 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C3' G 21018 " pdb=" C4' G 21018 " pdb=" O3' G 21018 " pdb=" C2' G 21018 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C3' G 21274 " pdb=" C4' G 21274 " pdb=" O3' G 21274 " pdb=" C2' G 21274 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 4233 not shown) Planarity restraints: 2639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21331 " -0.049 2.00e-02 2.50e+03 2.05e-02 1.27e+01 pdb=" N9 G 21331 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G 21331 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G 21331 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 21331 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 21331 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G 21331 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 21331 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G 21331 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G 21331 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G 21331 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 21331 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 987 " -0.040 2.00e-02 2.50e+03 1.74e-02 9.06e+00 pdb=" N9 G 2 987 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G 2 987 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 987 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 2 987 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G 2 987 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G 2 987 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 2 987 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 2 987 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G 2 987 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G 2 987 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G 2 987 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 930 " 0.037 2.00e-02 2.50e+03 1.80e-02 8.91e+00 pdb=" N9 A 2 930 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A 2 930 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A 2 930 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 930 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A 2 930 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A 2 930 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 2 930 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 930 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 930 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 2 930 " -0.005 2.00e-02 2.50e+03 ... (remaining 2636 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 146 2.54 - 3.13: 15567 3.13 - 3.72: 35035 3.72 - 4.31: 54789 4.31 - 4.90: 81496 Nonbonded interactions: 187033 Sorted by model distance: nonbonded pdb=" OP2 G 21172 " pdb="MG MG 21402 " model vdw 1.948 2.170 nonbonded pdb=" O6 G 21196 " pdb="MG MG 21403 " model vdw 1.968 2.170 nonbonded pdb=" OP1 C 21277 " pdb="MG MG 21406 " model vdw 2.071 2.170 nonbonded pdb=" OP1 G 21171 " pdb="MG MG 21402 " model vdw 2.132 2.170 nonbonded pdb=" O2' G 21155 " pdb=" O5' G 21156 " model vdw 2.132 3.040 ... (remaining 187028 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.010 0.089 24160 Z= 0.463 Angle : 1.230 55.177 34900 Z= 0.542 Chirality : 0.103 0.364 4236 Planarity : 0.006 0.062 2639 Dihedral : 21.025 146.947 10839 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 1.17 % Allowed : 11.08 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.83 (0.17), residues: 1497 helix: -2.93 (0.17), residues: 510 sheet: -3.39 (0.29), residues: 183 loop : -3.42 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 79 TYR 0.020 0.003 TYR U 150 PHE 0.047 0.003 PHE H 180 TRP 0.009 0.002 TRP L 64 HIS 0.010 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00990 / 0.46 (24156) covalent geometry : angle 1.16711 / 0.54 (34894) hydrogen bonds : bond 0.21887 / 11.35 ( 712) hydrogen bonds : angle 6.50632 / 2.69 ( 1661) metal coordination : bond 0.02346 / 1.17 ( 4) metal coordination : angle 29.67681 / 9.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 0.542 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: H 215 ARG cc_start: 0.7313 (mtt90) cc_final: 0.5259 (ppt170) REVERT: S 34 LYS cc_start: 0.8830 (tppp) cc_final: 0.8275 (tppt) REVERT: S 37 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7216 (mm-30) REVERT: Y 31 MET cc_start: 0.6659 (tpp) cc_final: 0.6246 (tpt) REVERT: Z 186 ASP cc_start: 0.7301 (p0) cc_final: 0.7010 (p0) REVERT: 3 32 ILE cc_start: 0.4356 (mm) cc_final: 0.3966 (mm) outliers start: 15 outliers final: 5 residues processed: 319 average time/residue: 0.1850 time to fit residues: 86.8100 Evaluate side-chains 238 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 233 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 6 residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 69 ASN H 129 ASN K 117 HIS L 84 GLN O 58 GLN S 30 HIS S 31 ASN S 48 ASN T 84 HIS U 18 GLN X 26 GLN Z 72 GLN Z 123 ASN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.070860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052034 restraints weight = 75341.398| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.48 r_work: 0.2730 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24160 Z= 0.183 Angle : 1.271 29.539 34900 Z= 0.510 Chirality : 0.109 1.429 4236 Planarity : 0.005 0.054 2639 Dihedral : 18.911 168.293 7623 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.87 % Allowed : 15.13 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -3.42 (0.19), residues: 1497 helix: -1.45 (0.22), residues: 525 sheet: -2.36 (0.31), residues: 198 loop : -2.90 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 3 119 TYR 0.011 0.001 TYR Y 45 PHE 0.013 0.001 PHE Y 21 TRP 0.009 0.001 TRP O 23 HIS 0.004 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (24156) covalent geometry : angle 1.25556 / 0.51 (34894) hydrogen bonds : bond 0.06207 / 3.18 ( 712) hydrogen bonds : angle 4.14480 / 1.72 ( 1661) metal coordination : bond 0.00966 / 0.48 ( 4) metal coordination : angle 15.33068 / 5.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8975 (t0) cc_final: 0.8673 (t70) REVERT: H 135 ASP cc_start: 0.8607 (t0) cc_final: 0.8272 (t0) REVERT: H 136 THR cc_start: 0.9147 (t) cc_final: 0.8940 (p) REVERT: H 215 ARG cc_start: 0.8536 (mtt90) cc_final: 0.5496 (ppt170) REVERT: K 103 ASP cc_start: 0.8680 (t0) cc_final: 0.8469 (t0) REVERT: L 17 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8490 (mm-30) REVERT: L 78 ASP cc_start: 0.9488 (m-30) cc_final: 0.9175 (t0) REVERT: L 84 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9312 (mt0) REVERT: O 46 ASP cc_start: 0.9249 (t0) cc_final: 0.9021 (t0) REVERT: S 15 GLU cc_start: 0.9169 (tp30) cc_final: 0.8696 (tp30) REVERT: S 23 GLU cc_start: 0.9122 (tp30) cc_final: 0.8877 (tp30) REVERT: S 59 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8795 (ttp80) REVERT: T 70 MET cc_start: 0.8971 (tpt) cc_final: 0.8761 (tpt) REVERT: T 93 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7815 (tm-30) REVERT: T 94 ILE cc_start: 0.9477 (mt) cc_final: 0.9152 (mm) REVERT: T 98 MET cc_start: 0.8697 (mtt) cc_final: 0.8483 (mtm) REVERT: T 124 ARG cc_start: 0.9394 (ttm110) cc_final: 0.9168 (tpp80) REVERT: U 30 GLU cc_start: 0.9047 (pp20) cc_final: 0.8712 (pp20) REVERT: U 49 ASP cc_start: 0.8787 (p0) cc_final: 0.8458 (p0) REVERT: X 10 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7744 (tm-30) REVERT: X 53 ASP cc_start: 0.8336 (m-30) cc_final: 0.8006 (m-30) REVERT: Y 18 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7399 (ttmt) REVERT: Y 30 PHE cc_start: 0.8568 (m-80) cc_final: 0.8232 (m-80) REVERT: Y 31 MET cc_start: 0.4975 (tpp) cc_final: 0.4751 (tpp) REVERT: Y 45 TYR cc_start: 0.7918 (m-80) cc_final: 0.7008 (m-80) REVERT: Z 30 TYR cc_start: 0.8916 (t80) cc_final: 0.8671 (t80) REVERT: Z 50 ASN cc_start: 0.9171 (t0) cc_final: 0.8965 (t0) REVERT: 3 66 LEU cc_start: 0.8576 (mm) cc_final: 0.8341 (tp) REVERT: 3 121 LEU cc_start: 0.8362 (tt) cc_final: 0.7912 (tt) REVERT: 3 122 MET cc_start: 0.6522 (mmp) cc_final: 0.5517 (ppp) outliers start: 24 outliers final: 12 residues processed: 286 average time/residue: 0.1575 time to fit residues: 69.5194 Evaluate side-chains 263 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 250 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 84 GLN Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [189, 62, 20, 102, 94, 44, 159, 57, 116, 53, 160] chunk 189 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 55 HIS U 18 GLN Z 72 GLN Z 101 GLN Z 123 ASN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.072308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053476 restraints weight = 75915.344| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.38 r_work: 0.2775 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24160 Z= 0.150 Angle : 1.010 20.755 34900 Z= 0.412 Chirality : 0.085 1.061 4236 Planarity : 0.005 0.041 2639 Dihedral : 18.667 173.748 7618 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.81 % Allowed : 16.15 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -2.58 (0.20), residues: 1497 helix: -0.62 (0.23), residues: 530 sheet: -1.71 (0.33), residues: 197 loop : -2.56 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 9 TYR 0.012 0.001 TYR Y 45 PHE 0.009 0.001 PHE Z 146 TRP 0.010 0.001 TRP Y 5 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (24156) covalent geometry : angle 0.99832 / 0.41 (34894) hydrogen bonds : bond 0.05566 / 2.83 ( 712) hydrogen bonds : angle 3.58179 / 1.49 ( 1661) metal coordination : bond 0.00778 / 0.39 ( 4) metal coordination : angle 11.53751 / 3.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 THR cc_start: 0.9320 (t) cc_final: 0.9069 (p) REVERT: H 135 ASP cc_start: 0.8639 (t0) cc_final: 0.8171 (t0) REVERT: H 136 THR cc_start: 0.9260 (t) cc_final: 0.8855 (p) REVERT: H 215 ARG cc_start: 0.8404 (mtt90) cc_final: 0.5714 (ttp80) REVERT: K 103 ASP cc_start: 0.8788 (t0) cc_final: 0.8420 (t0) REVERT: L 97 GLU cc_start: 0.8648 (tt0) cc_final: 0.7909 (tm-30) REVERT: O 15 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8487 (pp) REVERT: O 46 ASP cc_start: 0.9262 (t0) cc_final: 0.8990 (t0) REVERT: O 56 ASP cc_start: 0.8820 (p0) cc_final: 0.8608 (p0) REVERT: S 6 GLN cc_start: 0.8996 (mt0) cc_final: 0.8692 (mt0) REVERT: S 15 GLU cc_start: 0.9269 (tp30) cc_final: 0.8813 (tp30) REVERT: S 23 GLU cc_start: 0.9214 (tp30) cc_final: 0.8624 (tp30) REVERT: S 59 ARG cc_start: 0.9206 (ttp80) cc_final: 0.8768 (ttp80) REVERT: T 70 MET cc_start: 0.8923 (tpt) cc_final: 0.8513 (tpp) REVERT: T 93 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7811 (tm-30) REVERT: T 94 ILE cc_start: 0.9410 (mt) cc_final: 0.9025 (mm) REVERT: T 124 ARG cc_start: 0.9356 (ttm110) cc_final: 0.9082 (tpp80) REVERT: U 30 GLU cc_start: 0.8964 (pp20) cc_final: 0.8731 (tm-30) REVERT: U 49 ASP cc_start: 0.8800 (p0) cc_final: 0.8441 (p0) REVERT: X 53 ASP cc_start: 0.8451 (m-30) cc_final: 0.8084 (m-30) REVERT: Y 18 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7340 (ttmt) REVERT: Y 19 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6338 (p0) REVERT: Y 30 PHE cc_start: 0.8457 (m-80) cc_final: 0.8007 (m-80) REVERT: Y 31 MET cc_start: 0.4968 (tpp) cc_final: 0.4047 (tpp) REVERT: Y 45 TYR cc_start: 0.8080 (m-80) cc_final: 0.6994 (m-80) REVERT: Z 50 ASN cc_start: 0.9202 (t0) cc_final: 0.8988 (t0) REVERT: 3 25 ILE cc_start: 0.9211 (mp) cc_final: 0.8985 (tp) REVERT: 3 85 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: 3 121 LEU cc_start: 0.8199 (tt) cc_final: 0.7900 (tt) REVERT: 3 122 MET cc_start: 0.6531 (mmp) cc_final: 0.5833 (ppp) outliers start: 36 outliers final: 19 residues processed: 282 average time/residue: 0.1585 time to fit residues: 68.7692 Evaluate side-chains 262 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 19 ASN Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 6 residue 13 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [9, 97, 109, 135, 121, 125, 165, 130, 14, 0, 61] chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 94 ASN L 2 GLN L 84 GLN Z 72 GLN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049645 restraints weight = 76957.040| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.39 r_work: 0.2676 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24160 Z= 0.240 Angle : 1.068 24.940 34900 Z= 0.439 Chirality : 0.088 0.909 4236 Planarity : 0.005 0.040 2639 Dihedral : 18.776 176.058 7617 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.04 % Allowed : 17.08 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -2.14 (0.21), residues: 1497 helix: -0.22 (0.23), residues: 530 sheet: -1.31 (0.34), residues: 204 loop : -2.39 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 9 TYR 0.013 0.001 TYR Z 30 PHE 0.018 0.002 PHE H 180 TRP 0.008 0.001 TRP O 77 HIS 0.004 0.001 HIS P 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (24156) covalent geometry : angle 1.05624 / 0.44 (34894) hydrogen bonds : bond 0.05985 / 3.06 ( 712) hydrogen bonds : angle 3.58522 / 1.47 ( 1661) metal coordination : bond 0.01300 / 0.65 ( 4) metal coordination : angle 12.32868 / 4.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.8944 (t0) cc_final: 0.8718 (t0) REVERT: H 135 ASP cc_start: 0.8634 (t0) cc_final: 0.8146 (t0) REVERT: H 136 THR cc_start: 0.9281 (t) cc_final: 0.8894 (p) REVERT: H 215 ARG cc_start: 0.8424 (mtt180) cc_final: 0.5770 (ptt90) REVERT: K 103 ASP cc_start: 0.8929 (t0) cc_final: 0.8460 (t0) REVERT: O 15 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8407 (pp) REVERT: O 46 ASP cc_start: 0.9305 (t0) cc_final: 0.9051 (t0) REVERT: O 107 MET cc_start: 0.9480 (mmm) cc_final: 0.9222 (mmp) REVERT: S 15 GLU cc_start: 0.9345 (tp30) cc_final: 0.8937 (tp30) REVERT: S 23 GLU cc_start: 0.9332 (tp30) cc_final: 0.8739 (tp30) REVERT: S 59 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8625 (ttp80) REVERT: S 62 GLU cc_start: 0.9073 (pt0) cc_final: 0.8470 (pm20) REVERT: T 17 MET cc_start: 0.9126 (tpp) cc_final: 0.8668 (tpt) REVERT: T 70 MET cc_start: 0.9007 (tpt) cc_final: 0.8537 (tpp) REVERT: T 93 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8104 (tm-30) REVERT: T 94 ILE cc_start: 0.9288 (mt) cc_final: 0.8933 (mm) REVERT: U 49 ASP cc_start: 0.8905 (p0) cc_final: 0.8553 (p0) REVERT: X 33 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8057 (pp20) REVERT: X 53 ASP cc_start: 0.8510 (m-30) cc_final: 0.8173 (m-30) REVERT: X 59 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8460 (mt-10) REVERT: Y 1 MET cc_start: 0.5958 (tpp) cc_final: 0.5574 (tpt) REVERT: Y 18 LYS cc_start: 0.7731 (ttmt) cc_final: 0.7364 (ttmt) REVERT: Y 19 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6890 (p0) REVERT: Y 20 LYS cc_start: 0.8481 (pptt) cc_final: 0.8233 (pptt) REVERT: Y 42 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.7867 (tmm-80) REVERT: Y 45 TYR cc_start: 0.8233 (m-80) cc_final: 0.7252 (m-80) REVERT: Z 79 GLN cc_start: 0.8690 (mt0) cc_final: 0.8046 (pt0) REVERT: Z 148 GLN cc_start: 0.9305 (tp40) cc_final: 0.9041 (tp40) REVERT: 3 85 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8587 (pm20) outliers start: 39 outliers final: 27 residues processed: 269 average time/residue: 0.1699 time to fit residues: 70.4816 Evaluate side-chains 263 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 19 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 6 residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [104, 30, 96, 115, 129, 13, 141, 9, 14, 105, 76] chunk 104 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 2 GLN P 41 HIS ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053439 restraints weight = 76097.046| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.51 r_work: 0.2788 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24160 Z= 0.135 Angle : 0.947 18.243 34900 Z= 0.387 Chirality : 0.077 0.612 4236 Planarity : 0.005 0.052 2639 Dihedral : 18.657 178.049 7617 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.20 % Allowed : 17.78 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -1.72 (0.21), residues: 1497 helix: 0.09 (0.24), residues: 530 sheet: -1.00 (0.34), residues: 215 loop : -2.15 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 3 108 TYR 0.010 0.001 TYR Z 30 PHE 0.011 0.001 PHE Y 21 TRP 0.007 0.001 TRP Y 5 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (24156) covalent geometry : angle 0.93776 / 0.39 (34894) hydrogen bonds : bond 0.05301 / 2.69 ( 712) hydrogen bonds : angle 3.32107 / 1.35 ( 1661) metal coordination : bond 0.00724 / 0.36 ( 4) metal coordination : angle 9.88030 / 3.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 135 ASP cc_start: 0.8548 (t0) cc_final: 0.8177 (t0) REVERT: H 136 THR cc_start: 0.9300 (t) cc_final: 0.8977 (p) REVERT: H 215 ARG cc_start: 0.8430 (mtt180) cc_final: 0.5759 (ttp80) REVERT: K 103 ASP cc_start: 0.8911 (t0) cc_final: 0.8528 (t0) REVERT: L 43 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8787 (tttp) REVERT: O 15 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8424 (pp) REVERT: O 46 ASP cc_start: 0.9286 (t0) cc_final: 0.9009 (t0) REVERT: O 107 MET cc_start: 0.9437 (mmm) cc_final: 0.9144 (mmp) REVERT: S 6 GLN cc_start: 0.9010 (mt0) cc_final: 0.8753 (mt0) REVERT: S 15 GLU cc_start: 0.9345 (tp30) cc_final: 0.8959 (tp30) REVERT: S 23 GLU cc_start: 0.9346 (tp30) cc_final: 0.8776 (tp30) REVERT: S 59 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8748 (ttp80) REVERT: T 17 MET cc_start: 0.9148 (tpp) cc_final: 0.8789 (tpt) REVERT: T 70 MET cc_start: 0.9007 (tpt) cc_final: 0.8564 (tpp) REVERT: T 93 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8023 (tm-30) REVERT: T 94 ILE cc_start: 0.9314 (mt) cc_final: 0.8970 (mm) REVERT: U 49 ASP cc_start: 0.8852 (p0) cc_final: 0.8500 (p0) REVERT: X 33 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8090 (pp20) REVERT: X 53 ASP cc_start: 0.8523 (m-30) cc_final: 0.8228 (m-30) REVERT: X 59 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8520 (mt-10) REVERT: Y 1 MET cc_start: 0.5505 (tpp) cc_final: 0.4997 (tpt) REVERT: Y 18 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7239 (ttmt) REVERT: Y 19 ASN cc_start: 0.7150 (OUTLIER) cc_final: 0.6390 (p0) REVERT: Y 30 PHE cc_start: 0.8381 (m-80) cc_final: 0.7926 (m-10) REVERT: Y 42 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.7895 (tmm-80) REVERT: Y 45 TYR cc_start: 0.8148 (m-80) cc_final: 0.7116 (m-80) REVERT: Z 79 GLN cc_start: 0.8582 (mt0) cc_final: 0.7931 (pt0) REVERT: Z 148 GLN cc_start: 0.9261 (tp40) cc_final: 0.8942 (tp40) REVERT: 3 25 ILE cc_start: 0.9252 (mp) cc_final: 0.9024 (tt) REVERT: 3 85 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: 3 122 MET cc_start: 0.6415 (mmm) cc_final: 0.5260 (ppp) outliers start: 41 outliers final: 24 residues processed: 280 average time/residue: 0.1536 time to fit residues: 66.7178 Evaluate side-chains 265 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 19 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 6 residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [63, 92, 42, 98, 84, 47, 122, 3, 80, 67, 170] chunk 63 optimal weight: 0.0040 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 94 ASN X 26 GLN ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.049003 restraints weight = 77049.511| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.46 r_work: 0.2678 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24160 Z= 0.283 Angle : 1.081 22.809 34900 Z= 0.444 Chirality : 0.087 0.744 4236 Planarity : 0.005 0.046 2639 Dihedral : 18.856 179.239 7617 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.51 % Allowed : 18.49 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -1.51 (0.21), residues: 1497 helix: 0.37 (0.24), residues: 517 sheet: -0.78 (0.35), residues: 203 loop : -2.09 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 108 TYR 0.013 0.001 TYR U 63 PHE 0.019 0.002 PHE H 180 TRP 0.008 0.001 TRP O 77 HIS 0.004 0.001 HIS T 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.28 (24156) covalent geometry : angle 1.06936 / 0.44 (34894) hydrogen bonds : bond 0.06391 / 3.27 ( 712) hydrogen bonds : angle 3.60696 / 1.45 ( 1661) metal coordination : bond 0.01529 / 0.76 ( 4) metal coordination : angle 11.89242 / 3.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8507 (tp30) REVERT: H 135 ASP cc_start: 0.8594 (t0) cc_final: 0.8139 (t0) REVERT: H 215 ARG cc_start: 0.8604 (mtt180) cc_final: 0.5896 (ptm160) REVERT: K 103 ASP cc_start: 0.9000 (t0) cc_final: 0.8574 (t0) REVERT: L 34 MET cc_start: 0.9154 (ttp) cc_final: 0.8828 (tmm) REVERT: L 76 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8164 (mp0) REVERT: L 99 GLU cc_start: 0.8083 (pp20) cc_final: 0.7764 (tm-30) REVERT: O 15 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8436 (pp) REVERT: O 46 ASP cc_start: 0.9300 (t0) cc_final: 0.9075 (t0) REVERT: O 104 GLU cc_start: 0.9249 (tp30) cc_final: 0.8881 (tp30) REVERT: O 107 MET cc_start: 0.9497 (mmm) cc_final: 0.9234 (mmp) REVERT: S 15 GLU cc_start: 0.9374 (tp30) cc_final: 0.9016 (tp30) REVERT: S 23 GLU cc_start: 0.9416 (tp30) cc_final: 0.8920 (tp30) REVERT: S 59 ARG cc_start: 0.9200 (ttp80) cc_final: 0.8610 (ttp80) REVERT: S 62 GLU cc_start: 0.9150 (pt0) cc_final: 0.8483 (pm20) REVERT: T 17 MET cc_start: 0.9227 (tpp) cc_final: 0.8831 (tpt) REVERT: T 70 MET cc_start: 0.9088 (tpt) cc_final: 0.8564 (tpp) REVERT: T 93 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8215 (tm-30) REVERT: T 94 ILE cc_start: 0.9338 (mt) cc_final: 0.9061 (mm) REVERT: U 49 ASP cc_start: 0.8942 (p0) cc_final: 0.8284 (p0) REVERT: X 10 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8033 (tm-30) REVERT: X 33 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8197 (pp20) REVERT: X 53 ASP cc_start: 0.8535 (m-30) cc_final: 0.8162 (m-30) REVERT: Y 1 MET cc_start: 0.5814 (tpp) cc_final: 0.5178 (tpt) REVERT: Y 18 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7397 (ttmt) REVERT: Y 19 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6912 (p0) REVERT: Y 20 LYS cc_start: 0.8539 (pptt) cc_final: 0.8323 (pptt) REVERT: Y 42 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.7884 (tmm-80) REVERT: Y 45 TYR cc_start: 0.8316 (m-80) cc_final: 0.7296 (m-80) REVERT: Z 79 GLN cc_start: 0.8754 (mt0) cc_final: 0.8088 (pt0) REVERT: Z 148 GLN cc_start: 0.9398 (tp40) cc_final: 0.9040 (tp40) REVERT: 3 85 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8426 (pm20) outliers start: 45 outliers final: 31 residues processed: 270 average time/residue: 0.1584 time to fit residues: 65.9222 Evaluate side-chains 263 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 19 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 6 residue 13 VAL Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [133, 116, 138, 119, 89, 34, 8, 106, 161, 123, 112] chunk 133 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 89 optimal weight: 0.0000 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 18 GLN ** X 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053181 restraints weight = 75329.737| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.45 r_work: 0.2787 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24160 Z= 0.136 Angle : 0.938 18.302 34900 Z= 0.386 Chirality : 0.075 0.620 4236 Planarity : 0.004 0.048 2639 Dihedral : 18.714 178.070 7617 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.51 % Allowed : 19.19 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -1.27 (0.21), residues: 1497 helix: 0.53 (0.24), residues: 518 sheet: -0.59 (0.36), residues: 204 loop : -1.93 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 11 TYR 0.011 0.001 TYR S 53 PHE 0.011 0.001 PHE P 14 TRP 0.011 0.001 TRP Y 5 HIS 0.005 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (24156) covalent geometry : angle 0.93021 / 0.38 (34894) hydrogen bonds : bond 0.05407 / 2.75 ( 712) hydrogen bonds : angle 3.38552 / 1.36 ( 1661) metal coordination : bond 0.00793 / 0.40 ( 4) metal coordination : angle 9.49435 / 3.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8713 (tp30) REVERT: H 135 ASP cc_start: 0.8565 (t0) cc_final: 0.8165 (t0) REVERT: H 136 THR cc_start: 0.9279 (p) cc_final: 0.8813 (m) REVERT: H 215 ARG cc_start: 0.8184 (mtt180) cc_final: 0.5757 (ptt90) REVERT: K 103 ASP cc_start: 0.8936 (t0) cc_final: 0.8537 (t0) REVERT: L 34 MET cc_start: 0.9077 (ttp) cc_final: 0.8806 (tmm) REVERT: L 43 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8694 (tttp) REVERT: L 76 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8087 (mt-10) REVERT: L 99 GLU cc_start: 0.7957 (pp20) cc_final: 0.7694 (tm-30) REVERT: O 15 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8288 (pp) REVERT: O 46 ASP cc_start: 0.9273 (t0) cc_final: 0.8983 (t0) REVERT: O 104 GLU cc_start: 0.9196 (tp30) cc_final: 0.8832 (tp30) REVERT: O 107 MET cc_start: 0.9474 (mmm) cc_final: 0.9155 (mmt) REVERT: P 5 ASP cc_start: 0.9009 (m-30) cc_final: 0.8683 (m-30) REVERT: S 6 GLN cc_start: 0.9006 (mt0) cc_final: 0.8731 (mt0) REVERT: S 15 GLU cc_start: 0.9355 (tp30) cc_final: 0.8999 (tp30) REVERT: S 23 GLU cc_start: 0.9453 (tp30) cc_final: 0.8846 (tp30) REVERT: S 59 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8657 (ttp80) REVERT: S 62 GLU cc_start: 0.9143 (pt0) cc_final: 0.8537 (pm20) REVERT: T 17 MET cc_start: 0.9115 (tpp) cc_final: 0.8795 (tpt) REVERT: T 70 MET cc_start: 0.9085 (tpt) cc_final: 0.8531 (tpp) REVERT: T 88 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8295 (mm-30) REVERT: T 93 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8117 (tm-30) REVERT: T 94 ILE cc_start: 0.9310 (mt) cc_final: 0.9036 (mm) REVERT: U 49 ASP cc_start: 0.8815 (p0) cc_final: 0.8463 (p0) REVERT: X 10 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7943 (tm-30) REVERT: X 33 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: X 53 ASP cc_start: 0.8413 (m-30) cc_final: 0.8043 (m-30) REVERT: X 59 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8345 (mt-10) REVERT: Y 1 MET cc_start: 0.5276 (tpp) cc_final: 0.4929 (tpt) REVERT: Y 18 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7410 (ttmt) REVERT: Y 19 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6322 (p0) REVERT: Y 30 PHE cc_start: 0.8485 (m-80) cc_final: 0.7968 (m-80) REVERT: Y 45 TYR cc_start: 0.8176 (m-80) cc_final: 0.7067 (m-80) REVERT: Z 79 GLN cc_start: 0.8561 (mt0) cc_final: 0.7892 (pt0) REVERT: 3 85 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: 3 122 MET cc_start: 0.6261 (mmm) cc_final: 0.5667 (pmm) outliers start: 45 outliers final: 26 residues processed: 281 average time/residue: 0.1620 time to fit residues: 70.7319 Evaluate side-chains 278 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 19 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 51 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 66 LEU Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [184, 93, 56, 178, 94, 37, 133, 130, 85, 156, 149] chunk 184 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 178 optimal weight: 0.0870 chunk 94 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 65 HIS ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052008 restraints weight = 75229.295| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.53 r_work: 0.2756 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24160 Z= 0.171 Angle : 0.962 20.281 34900 Z= 0.396 Chirality : 0.077 0.658 4236 Planarity : 0.004 0.049 2639 Dihedral : 18.686 178.181 7617 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.89 % Allowed : 20.83 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -1.12 (0.22), residues: 1497 helix: 0.59 (0.24), residues: 521 sheet: -0.44 (0.36), residues: 204 loop : -1.83 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 11 TYR 0.013 0.001 TYR S 53 PHE 0.012 0.001 PHE Y 21 TRP 0.007 0.001 TRP Y 38 HIS 0.005 0.001 HIS 3 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (24156) covalent geometry : angle 0.95264 / 0.40 (34894) hydrogen bonds : bond 0.05523 / 2.81 ( 712) hydrogen bonds : angle 3.39150 / 1.34 ( 1661) metal coordination : bond 0.00998 / 0.50 ( 4) metal coordination : angle 10.07432 / 3.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8711 (tp30) REVERT: H 135 ASP cc_start: 0.8667 (t0) cc_final: 0.8235 (t0) REVERT: H 136 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8753 (m) REVERT: H 215 ARG cc_start: 0.8353 (mtt180) cc_final: 0.5959 (ptt90) REVERT: K 103 ASP cc_start: 0.8962 (t0) cc_final: 0.8539 (t0) REVERT: L 34 MET cc_start: 0.9057 (ttp) cc_final: 0.8819 (tmm) REVERT: L 43 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8734 (tttp) REVERT: L 76 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8137 (mp0) REVERT: L 99 GLU cc_start: 0.8020 (pp20) cc_final: 0.7741 (tm-30) REVERT: O 15 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8316 (pp) REVERT: O 46 ASP cc_start: 0.9271 (t0) cc_final: 0.8987 (t0) REVERT: O 104 GLU cc_start: 0.9271 (tp30) cc_final: 0.8906 (tp30) REVERT: O 107 MET cc_start: 0.9491 (mmm) cc_final: 0.9220 (mmp) REVERT: P 5 ASP cc_start: 0.9027 (m-30) cc_final: 0.8696 (m-30) REVERT: S 6 GLN cc_start: 0.9055 (mt0) cc_final: 0.8798 (mt0) REVERT: S 15 GLU cc_start: 0.9408 (tp30) cc_final: 0.9087 (tp30) REVERT: S 23 GLU cc_start: 0.9426 (tp30) cc_final: 0.8780 (tp30) REVERT: S 59 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8653 (ttp80) REVERT: S 62 GLU cc_start: 0.9130 (pt0) cc_final: 0.8473 (pm20) REVERT: T 17 MET cc_start: 0.9148 (tpp) cc_final: 0.8830 (tpt) REVERT: T 70 MET cc_start: 0.9086 (tpt) cc_final: 0.8506 (tpp) REVERT: T 93 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8130 (tm-30) REVERT: T 94 ILE cc_start: 0.9288 (mt) cc_final: 0.9001 (mm) REVERT: U 49 ASP cc_start: 0.8895 (p0) cc_final: 0.8216 (p0) REVERT: X 10 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7754 (tm-30) REVERT: X 33 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: X 53 ASP cc_start: 0.8423 (m-30) cc_final: 0.8076 (m-30) REVERT: X 59 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8341 (mt-10) REVERT: Y 1 MET cc_start: 0.5583 (tpp) cc_final: 0.5144 (tpt) REVERT: Y 18 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7486 (ttmt) REVERT: Y 19 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6830 (p0) REVERT: Y 42 ARG cc_start: 0.8455 (tmm-80) cc_final: 0.7821 (tmm-80) REVERT: Y 45 TYR cc_start: 0.8277 (m-80) cc_final: 0.7149 (m-80) REVERT: Z 79 GLN cc_start: 0.8574 (mt0) cc_final: 0.7927 (pt0) REVERT: 3 82 SER cc_start: 0.6644 (t) cc_final: 0.6276 (t) REVERT: 3 85 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: 3 92 ILE cc_start: 0.6899 (tt) cc_final: 0.6649 (mt) REVERT: 3 122 MET cc_start: 0.6170 (mmm) cc_final: 0.5568 (pmm) outliers start: 37 outliers final: 26 residues processed: 270 average time/residue: 0.1623 time to fit residues: 67.3905 Evaluate side-chains 277 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 19 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 66 LEU Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [148, 54, 28, 157, 111, 57, 139, 66, 0, 99, 91] chunk 148 optimal weight: 0.0010 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 111 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 48 HIS H 55 HIS 3 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057312 restraints weight = 75230.454| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.58 r_work: 0.2890 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24160 Z= 0.125 Angle : 0.894 14.672 34900 Z= 0.369 Chirality : 0.070 0.567 4236 Planarity : 0.004 0.052 2639 Dihedral : 18.482 176.756 7617 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.65 % Allowed : 21.45 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.92 (0.22), residues: 1497 helix: 0.72 (0.24), residues: 512 sheet: -0.21 (0.37), residues: 197 loop : -1.68 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 11 TYR 0.008 0.001 TYR H 101 PHE 0.009 0.001 PHE Y 21 TRP 0.015 0.001 TRP Y 5 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (24156) covalent geometry : angle 0.88911 / 0.37 (34894) hydrogen bonds : bond 0.05111 / 2.59 ( 712) hydrogen bonds : angle 3.21080 / 1.26 ( 1661) metal coordination : bond 0.00598 / 0.30 ( 4) metal coordination : angle 7.48125 / 2.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8704 (tp30) REVERT: H 135 ASP cc_start: 0.8597 (t0) cc_final: 0.8198 (t0) REVERT: H 136 THR cc_start: 0.9291 (p) cc_final: 0.8861 (m) REVERT: H 215 ARG cc_start: 0.8046 (mtt180) cc_final: 0.5734 (ptt90) REVERT: K 103 ASP cc_start: 0.8932 (t0) cc_final: 0.8564 (t0) REVERT: L 3 LYS cc_start: 0.8682 (mmmt) cc_final: 0.7802 (mmmt) REVERT: L 43 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8869 (tttp) REVERT: L 76 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8318 (mm-30) REVERT: L 99 GLU cc_start: 0.7905 (pp20) cc_final: 0.7653 (tm-30) REVERT: O 46 ASP cc_start: 0.9215 (t0) cc_final: 0.8899 (t0) REVERT: O 86 GLU cc_start: 0.8847 (tp30) cc_final: 0.8595 (mm-30) REVERT: O 104 GLU cc_start: 0.9233 (tp30) cc_final: 0.8871 (tp30) REVERT: O 107 MET cc_start: 0.9458 (mmm) cc_final: 0.9146 (mmt) REVERT: P 5 ASP cc_start: 0.9023 (m-30) cc_final: 0.8803 (m-30) REVERT: P 8 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8833 (mtmm) REVERT: P 12 ARG cc_start: 0.8755 (mmt90) cc_final: 0.8539 (mpt180) REVERT: S 6 GLN cc_start: 0.9022 (mt0) cc_final: 0.8683 (mt0) REVERT: S 15 GLU cc_start: 0.9349 (tp30) cc_final: 0.9094 (tp30) REVERT: S 23 GLU cc_start: 0.9440 (tp30) cc_final: 0.8859 (tp30) REVERT: S 34 LYS cc_start: 0.9385 (tppp) cc_final: 0.9040 (tppt) REVERT: S 59 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8708 (ttp80) REVERT: S 62 GLU cc_start: 0.9136 (pt0) cc_final: 0.8480 (pm20) REVERT: T 17 MET cc_start: 0.9115 (tpp) cc_final: 0.8781 (tpt) REVERT: T 93 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8081 (tm-30) REVERT: T 94 ILE cc_start: 0.9239 (mt) cc_final: 0.8927 (mm) REVERT: U 49 ASP cc_start: 0.8794 (p0) cc_final: 0.8423 (p0) REVERT: X 10 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7630 (tm-30) REVERT: X 11 VAL cc_start: 0.9439 (t) cc_final: 0.8977 (p) REVERT: X 33 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: X 53 ASP cc_start: 0.8336 (m-30) cc_final: 0.7896 (m-30) REVERT: X 59 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8425 (mt-10) REVERT: Y 1 MET cc_start: 0.4465 (tpp) cc_final: 0.3726 (tpt) REVERT: Y 6 LYS cc_start: 0.6361 (mmtt) cc_final: 0.5898 (mmpt) REVERT: Y 18 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7548 (ttmt) REVERT: Y 30 PHE cc_start: 0.8501 (m-80) cc_final: 0.8031 (m-10) REVERT: Y 42 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7644 (tmm-80) REVERT: Y 45 TYR cc_start: 0.8220 (m-80) cc_final: 0.6947 (m-80) REVERT: Z 79 GLN cc_start: 0.8494 (mt0) cc_final: 0.7877 (pt0) REVERT: Z 83 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8585 (mt0) REVERT: Z 117 MET cc_start: 0.8996 (ttp) cc_final: 0.8790 (ttp) REVERT: Z 148 GLN cc_start: 0.9181 (tp40) cc_final: 0.8848 (tp40) REVERT: 3 15 LEU cc_start: 0.6273 (pt) cc_final: 0.5555 (mp) REVERT: 3 82 SER cc_start: 0.6734 (t) cc_final: 0.6398 (t) REVERT: 3 85 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: 3 122 MET cc_start: 0.6524 (mmm) cc_final: 0.6047 (pmm) outliers start: 34 outliers final: 23 residues processed: 288 average time/residue: 0.1633 time to fit residues: 72.2652 Evaluate side-chains 267 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 8 LYS Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 66 LEU Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 86 LEU Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [168, 152, 160, 103, 185, 43, 45, 109, 125, 147, 49] chunk 168 optimal weight: 0.9990 chunk 152 optimal weight: 0.0870 chunk 160 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 25 GLN X 26 GLN 3 65 HIS ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054014 restraints weight = 75314.566| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.56 r_work: 0.2795 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24160 Z= 0.157 Angle : 0.930 18.602 34900 Z= 0.384 Chirality : 0.073 0.624 4236 Planarity : 0.004 0.050 2639 Dihedral : 18.504 177.117 7617 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.50 % Allowed : 22.39 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.76 (0.22), residues: 1497 helix: 0.89 (0.24), residues: 510 sheet: -0.13 (0.37), residues: 204 loop : -1.60 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 11 TYR 0.015 0.001 TYR H 101 PHE 0.012 0.001 PHE Y 21 TRP 0.010 0.001 TRP Y 38 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (24156) covalent geometry : angle 0.92181 / 0.38 (34894) hydrogen bonds : bond 0.05284 / 2.69 ( 712) hydrogen bonds : angle 3.32393 / 1.30 ( 1661) metal coordination : bond 0.00855 / 0.43 ( 4) metal coordination : angle 9.42110 / 3.14 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2994 Ramachandran restraints generated. 1497 Oldfield, 0 Emsley, 1497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8723 (tp30) REVERT: H 135 ASP cc_start: 0.8599 (t0) cc_final: 0.8169 (t0) REVERT: H 136 THR cc_start: 0.9353 (p) cc_final: 0.8957 (m) REVERT: H 215 ARG cc_start: 0.8316 (mtt180) cc_final: 0.5908 (ptt90) REVERT: K 103 ASP cc_start: 0.8991 (t0) cc_final: 0.8553 (t0) REVERT: L 25 GLN cc_start: 0.9424 (OUTLIER) cc_final: 0.9115 (pp30) REVERT: L 43 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8773 (tttp) REVERT: L 76 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8170 (mp0) REVERT: L 99 GLU cc_start: 0.8000 (pp20) cc_final: 0.7686 (tm-30) REVERT: O 46 ASP cc_start: 0.9265 (t0) cc_final: 0.8989 (t0) REVERT: O 86 GLU cc_start: 0.8881 (tp30) cc_final: 0.8607 (mm-30) REVERT: O 104 GLU cc_start: 0.9271 (tp30) cc_final: 0.8909 (tp30) REVERT: O 107 MET cc_start: 0.9493 (mmm) cc_final: 0.9174 (mmt) REVERT: P 8 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8915 (mtmm) REVERT: P 9 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8470 (ttm-80) REVERT: S 6 GLN cc_start: 0.9102 (mt0) cc_final: 0.8831 (mt0) REVERT: S 15 GLU cc_start: 0.9368 (tp30) cc_final: 0.9116 (tp30) REVERT: S 23 GLU cc_start: 0.9438 (tp30) cc_final: 0.8823 (tp30) REVERT: S 59 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8706 (ttp80) REVERT: S 62 GLU cc_start: 0.9151 (pt0) cc_final: 0.8479 (pm20) REVERT: T 17 MET cc_start: 0.9142 (tpp) cc_final: 0.8817 (tpt) REVERT: T 93 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8102 (tm-30) REVERT: T 94 ILE cc_start: 0.9230 (mt) cc_final: 0.8941 (mm) REVERT: U 49 ASP cc_start: 0.8838 (p0) cc_final: 0.8155 (p0) REVERT: X 10 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7695 (tm-30) REVERT: X 33 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: X 53 ASP cc_start: 0.8379 (m-30) cc_final: 0.8077 (m-30) REVERT: X 59 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8412 (mt-10) REVERT: Y 1 MET cc_start: 0.4912 (tpp) cc_final: 0.4092 (tpt) REVERT: Y 30 PHE cc_start: 0.8553 (m-80) cc_final: 0.8046 (m-10) REVERT: Y 42 ARG cc_start: 0.8224 (tmm-80) cc_final: 0.7603 (tmm-80) REVERT: Y 45 TYR cc_start: 0.8262 (m-80) cc_final: 0.6955 (m-80) REVERT: Z 79 GLN cc_start: 0.8582 (mt0) cc_final: 0.8000 (pt0) REVERT: Z 83 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8698 (mt0) REVERT: Z 148 GLN cc_start: 0.9252 (tp40) cc_final: 0.8904 (tp40) REVERT: 3 15 LEU cc_start: 0.6230 (pt) cc_final: 0.5495 (mp) REVERT: 3 82 SER cc_start: 0.7020 (t) cc_final: 0.6683 (t) REVERT: 3 85 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8343 (pt0) outliers start: 32 outliers final: 23 residues processed: 266 average time/residue: 0.1632 time to fit residues: 67.5007 Evaluate side-chains 274 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain T residue 99 ILE Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain 3 residue 36 THR Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 66 LEU Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [117, 115, 137, 148, 164, 57, 58, 68, 113, 102, 16] chunk 117 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 25 GLN 3 65 HIS ** 6 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054810 restraints weight = 75684.979| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.61 r_work: 0.2835 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24160 Z= 0.137 Angle : 0.924 17.422 34900 Z= 0.382 Chirality : 0.072 0.608 4236 Planarity : 0.004 0.053 2639 Dihedral : 18.502 176.713 7617 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.34 % Allowed : 23.32 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: -0.71 (0.22), residues: 1497 helix: 0.89 (0.24), residues: 510 sheet: -0.06 (0.38), residues: 197 loop : -1.55 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 11 TYR 0.014 0.001 TYR H 101 PHE 0.012 0.001 PHE Y 21 TRP 0.010 0.001 TRP Y 38 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (24156) covalent geometry : angle 0.91691 / 0.38 (34894) hydrogen bonds : bond 0.05098 / 2.60 ( 712) hydrogen bonds : angle 3.28319 / 1.29 ( 1661) metal coordination : bond 0.00751 / 0.38 ( 4) metal coordination : angle 8.85947 / 2.95 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6266.29 seconds wall clock time: 107 minutes 34.34 seconds (6454.34 seconds total)