Starting phenix.real_space_refine on Fri Sep 27 06:00:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/09_2024/5tc1_8397.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/09_2024/5tc1_8397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/09_2024/5tc1_8397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/09_2024/5tc1_8397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/09_2024/5tc1_8397.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/09_2024/5tc1_8397.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 242 5.49 5 S 43 5.16 5 C 8768 2.51 5 N 2671 2.21 5 O 3669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15393 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122} Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "D" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122} Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "G" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 898 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "M" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2608 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 4 Chain: "R" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 5132 Classifications: {'RNA': 242} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 34, 'rna3p_pur': 92, 'rna3p_pyr': 89} Link IDs: {'rna2p': 61, 'rna3p': 180} Chain breaks: 15 Residues with excluded nonbonded symmetry interactions: 17 residue: pdb=" P A R1748 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1748 " occ=0.80 residue: pdb=" P U R1749 " occ=0.80 ... (18 atoms not shown) pdb=" C6 U R1749 " occ=0.80 residue: pdb=" P G R1750 " occ=0.80 ... (21 atoms not shown) pdb=" C4 G R1750 " occ=0.80 residue: pdb=" P A R1751 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1751 " occ=0.80 residue: pdb=" P G R1752 " occ=0.80 ... (21 atoms not shown) pdb=" C4 G R1752 " occ=0.80 residue: pdb=" P G R1753 " occ=0.80 ... (21 atoms not shown) pdb=" C4 G R1753 " occ=0.80 residue: pdb=" P A R1754 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1754 " occ=0.80 residue: pdb=" P U R1755 " occ=0.80 ... (18 atoms not shown) pdb=" C6 U R1755 " occ=0.80 residue: pdb=" P U R1756 " occ=0.80 ... (18 atoms not shown) pdb=" C6 U R1756 " occ=0.80 residue: pdb=" P A R1757 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1757 " occ=0.80 residue: pdb=" P C R1758 " occ=0.80 ... (18 atoms not shown) pdb=" C6 C R1758 " occ=0.80 residue: pdb=" P C R1759 " occ=0.80 ... (18 atoms not shown) pdb=" C6 C R1759 " occ=0.80 ... (remaining 5 not shown) Time building chain proxies: 9.97, per 1000 atoms: 0.65 Number of scatterers: 15393 At special positions: 0 Unit cell: (206.7, 216.24, 261.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 242 15.00 O 3669 8.00 N 2671 7.00 C 8768 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: 4.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 26.6% alpha, 40.5% beta 17 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.829A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.603A pdb=" N GLY B 28 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.692A pdb=" N VAL B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.532A pdb=" N ILE B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.847A pdb=" N GLY C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.623A pdb=" N ALA C 41 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 112 removed outlier: 3.554A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.603A pdb=" N LEU D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.514A pdb=" N ALA D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 removed outlier: 3.552A pdb=" N ALA E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.585A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.890A pdb=" N GLY F 28 " --> pdb=" O PHE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 112 removed outlier: 3.687A pdb=" N ILE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 112 " --> pdb=" O MET F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.530A pdb=" N ALA F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 removed outlier: 4.044A pdb=" N GLY G 28 " --> pdb=" O PHE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 removed outlier: 3.573A pdb=" N ALA G 41 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 112 removed outlier: 3.949A pdb=" N LEU G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.623A pdb=" N ALA G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 4.362A pdb=" N GLY H 28 " --> pdb=" O PHE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.590A pdb=" N LEU H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 105 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'M' and resid 98 through 104 removed outlier: 3.696A pdb=" N CYS M 101 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR M 102 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER M 103 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 104 " --> pdb=" O CYS M 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 98 through 104' Processing helix chain 'M' and resid 117 through 135 removed outlier: 4.056A pdb=" N ARG M 123 " --> pdb=" O ASN M 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 131 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR M 133 " --> pdb=" O LEU M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 145 through 150 Processing helix chain 'M' and resid 152 through 169 removed outlier: 3.580A pdb=" N GLN M 156 " --> pdb=" O GLN M 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 166 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 Processing helix chain 'M' and resid 191 through 199 removed outlier: 3.717A pdb=" N LEU M 199 " --> pdb=" O ARG M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 220 Proline residue: M 205 - end of helix removed outlier: 3.663A pdb=" N GLN M 211 " --> pdb=" O MET M 207 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU M 217 " --> pdb=" O ALA M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 224 Processing helix chain 'M' and resid 294 through 300 removed outlier: 3.741A pdb=" N ASP M 298 " --> pdb=" O SER M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 312 removed outlier: 3.503A pdb=" N MET M 306 " --> pdb=" O PRO M 302 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU M 308 " --> pdb=" O GLY M 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR M 311 " --> pdb=" O LEU M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 388 removed outlier: 3.722A pdb=" N ILE M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.710A pdb=" N VAL A 18 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 31 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 61 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG A 56 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 91 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 58 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 89 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 60 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 87 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 62 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 64 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 83 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 66 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 79 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 removed outlier: 7.131A pdb=" N VAL B 18 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ARG D 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL D 72 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN D 70 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA D 80 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA D 68 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP D 82 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 49 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU D 31 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 18 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.891A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 61 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP C 82 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 68 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA C 80 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN C 70 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL C 72 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 7 through 10 removed outlier: 5.262A pdb=" N VAL E 8 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 20 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 10 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU E 31 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 30 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ARG F 83 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 72 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN F 70 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA F 80 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA F 68 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP F 82 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 61 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU F 31 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 18 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 7 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 7 through 10 removed outlier: 5.262A pdb=" N VAL E 8 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 20 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 10 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU E 31 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 30 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ARG E 83 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 61 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU F 31 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 18 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 7 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.858A pdb=" N VAL G 18 " --> pdb=" O LEU G 9 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU G 31 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS G 46 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 61 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG G 49 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 51 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 90 " --> pdb=" O TYR G 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 10 removed outlier: 6.662A pdb=" N VAL H 18 " --> pdb=" O LEU H 9 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLU H 31 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS H 43 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 61 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN H 70 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 38 through 39 removed outlier: 6.745A pdb=" N LYS M 350 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 351 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 327 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TRP M 264 " --> pdb=" O MET M 319 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY M 321 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL M 262 " --> pdb=" O GLY M 321 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL M 323 " --> pdb=" O ARG M 260 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG M 260 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP M 325 " --> pdb=" O SER M 258 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER M 258 " --> pdb=" O ASP M 325 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE M 327 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN M 256 " --> pdb=" O ILE M 327 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY M 329 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR M 254 " --> pdb=" O GLY M 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE M 261 " --> pdb=" O ARG M 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 44 through 45 removed outlier: 4.067A pdb=" N PHE M 44 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER M 61 " --> pdb=" O PHE M 44 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR M 60 " --> pdb=" O ARG M 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 351 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 327 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA M 369 " --> pdb=" O CYS M 316 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3967 1.34 - 1.45: 4322 1.45 - 1.57: 7348 1.57 - 1.69: 468 1.69 - 1.81: 67 Bond restraints: 16172 Sorted by residual: bond pdb=" C LEU M 104 " pdb=" N PHE M 105 " ideal model delta sigma weight residual 1.330 1.232 0.098 1.47e-02 4.63e+03 4.49e+01 bond pdb=" C VAL E 20 " pdb=" N ALA E 21 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.59e-02 3.96e+03 1.37e+01 bond pdb=" C TYR F 129 " pdb=" O TYR F 129 " ideal model delta sigma weight residual 1.231 1.277 -0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" C TYR F 129 " pdb=" OXT TYR F 129 " ideal model delta sigma weight residual 1.231 1.277 -0.046 2.00e-02 2.50e+03 5.26e+00 bond pdb=" C ILE G 118 " pdb=" N PRO G 119 " ideal model delta sigma weight residual 1.335 1.350 -0.015 9.40e-03 1.13e+04 2.53e+00 ... (remaining 16167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 23046 3.92 - 7.83: 48 7.83 - 11.75: 5 11.75 - 15.67: 0 15.67 - 19.59: 1 Bond angle restraints: 23100 Sorted by residual: angle pdb=" C LEU M 104 " pdb=" N PHE M 105 " pdb=" CA PHE M 105 " ideal model delta sigma weight residual 120.68 140.27 -19.59 1.52e+00 4.33e-01 1.66e+02 angle pdb=" C LEU M 179 " pdb=" N ALA M 180 " pdb=" CA ALA M 180 " ideal model delta sigma weight residual 122.40 127.50 -5.10 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N VAL B 67 " pdb=" CA VAL B 67 " pdb=" C VAL B 67 " ideal model delta sigma weight residual 112.96 109.49 3.47 1.00e+00 1.00e+00 1.21e+01 angle pdb=" C ASN M 110 " pdb=" N LEU M 111 " pdb=" CA LEU M 111 " ideal model delta sigma weight residual 123.05 128.30 -5.25 1.57e+00 4.06e-01 1.12e+01 angle pdb=" C ALA H 26 " pdb=" N ASN H 27 " pdb=" CA ASN H 27 " ideal model delta sigma weight residual 122.40 127.18 -4.78 1.45e+00 4.76e-01 1.09e+01 ... (remaining 23095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 9141 35.56 - 71.12: 682 71.12 - 106.68: 89 106.68 - 142.24: 3 142.24 - 177.80: 14 Dihedral angle restraints: 9929 sinusoidal: 6026 harmonic: 3903 Sorted by residual: dihedral pdb=" C4' U R2479 " pdb=" C3' U R2479 " pdb=" C2' U R2479 " pdb=" C1' U R2479 " ideal model delta sinusoidal sigma weight residual -35.00 36.21 -71.21 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' U R2844 " pdb=" C3' U R2844 " pdb=" C2' U R2844 " pdb=" C1' U R2844 " ideal model delta sinusoidal sigma weight residual -35.00 36.16 -71.16 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' U R1755 " pdb=" C3' U R1755 " pdb=" C2' U R1755 " pdb=" C1' U R1755 " ideal model delta sinusoidal sigma weight residual -35.00 36.12 -71.12 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 9926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1962 0.054 - 0.109: 422 0.109 - 0.163: 289 0.163 - 0.217: 195 0.217 - 0.271: 3 Chirality restraints: 2871 Sorted by residual: chirality pdb=" CB VAL H 20 " pdb=" CA VAL H 20 " pdb=" CG1 VAL H 20 " pdb=" CG2 VAL H 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL F 20 " pdb=" CA VAL F 20 " pdb=" CG1 VAL F 20 " pdb=" CG2 VAL F 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2868 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 64 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO F 65 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 65 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 65 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 204 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO M 205 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO M 205 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 205 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 64 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO H 65 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " -0.035 5.00e-02 4.00e+02 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 14 1.88 - 2.64: 394 2.64 - 3.39: 19273 3.39 - 4.15: 37897 4.15 - 4.90: 61108 Nonbonded interactions: 118686 Sorted by model distance: nonbonded pdb=" NH1 ARG E 56 " pdb=" OD1 ASN F 125 " model vdw 1.126 3.120 nonbonded pdb=" OG SER M 58 " pdb=" O6 G R3555 " model vdw 1.430 3.040 nonbonded pdb=" O ALA B 1 " pdb=" CE2 TYR D 129 " model vdw 1.444 3.340 nonbonded pdb=" CB ALA B 1 " pdb=" OH TYR D 129 " model vdw 1.483 3.460 nonbonded pdb=" OD1 ASP E 114 " pdb=" NE2 GLN F 109 " model vdw 1.649 3.120 ... (remaining 118681 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'B' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'C' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'D' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'E' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'F' and (resid 1 through 67 or resid 78 through 129)) selection = chain 'G' selection = (chain 'H' and (resid 1 through 67 or resid 78 through 129)) } 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=0.80 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.006 0.098 16172 Z= 0.367 Angle : 0.870 19.587 23100 Z= 0.562 Chirality : 0.075 0.271 2871 Planarity : 0.007 0.068 2074 Dihedral : 22.119 177.798 7407 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.27 % Allowed : 1.25 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.19), residues: 1324 helix: -4.62 (0.09), residues: 332 sheet: -0.77 (0.25), residues: 423 loop : -2.45 (0.21), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 32 HIS 0.008 0.002 HIS M 55 PHE 0.028 0.004 PHE A 4 TYR 0.022 0.003 TYR A 42 ARG 0.007 0.001 ARG M 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8996 (tttt) cc_final: 0.8783 (tttm) REVERT: A 66 LYS cc_start: 0.8203 (tptt) cc_final: 0.7890 (tptm) REVERT: A 88 MET cc_start: 0.8541 (ptp) cc_final: 0.6644 (mmt) REVERT: A 100 ASP cc_start: 0.8671 (m-30) cc_final: 0.8392 (m-30) REVERT: A 106 LYS cc_start: 0.8835 (mttm) cc_final: 0.7469 (tmtt) REVERT: E 97 THR cc_start: 0.8850 (p) cc_final: 0.8602 (p) REVERT: E 128 ILE cc_start: 0.8729 (mm) cc_final: 0.8325 (mm) REVERT: F 12 ASN cc_start: 0.7832 (m-40) cc_final: 0.7523 (t0) REVERT: G 38 ARG cc_start: 0.8012 (tpm-80) cc_final: 0.6293 (ptt-90) REVERT: H 100 ASP cc_start: 0.8231 (m-30) cc_final: 0.7689 (m-30) REVERT: M 308 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7240 (mt-10) REVERT: M 350 LYS cc_start: 0.8329 (mttt) cc_final: 0.8079 (mtpp) outliers start: 3 outliers final: 1 residues processed: 335 average time/residue: 0.2647 time to fit residues: 130.8230 Evaluate side-chains 210 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 129 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN B 116 ASN C 98 ASN D 36 ASN F 6 GLN F 109 GLN G 54 GLN G 116 ASN H 70 GLN M 11 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 352 GLN M 357 HIS M 389 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16172 Z= 0.267 Angle : 0.697 8.314 23100 Z= 0.363 Chirality : 0.044 0.279 2871 Planarity : 0.006 0.049 2074 Dihedral : 23.602 179.507 5119 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.32 % Allowed : 10.88 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.20), residues: 1324 helix: -2.86 (0.19), residues: 327 sheet: -0.33 (0.24), residues: 428 loop : -1.89 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 54 HIS 0.002 0.001 HIS M 55 PHE 0.029 0.003 PHE M 105 TYR 0.014 0.002 TYR F 58 ARG 0.008 0.001 ARG E 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.566 Fit side-chains REVERT: A 88 MET cc_start: 0.8262 (ptp) cc_final: 0.6468 (mmt) REVERT: A 106 LYS cc_start: 0.8703 (mttm) cc_final: 0.7201 (tmtt) REVERT: E 128 ILE cc_start: 0.8900 (mm) cc_final: 0.8581 (mm) REVERT: F 12 ASN cc_start: 0.7800 (m-40) cc_final: 0.7482 (t0) REVERT: F 33 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8081 (pp) REVERT: F 56 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7365 (mtp180) REVERT: G 38 ARG cc_start: 0.8192 (tpm-80) cc_final: 0.6413 (ptt-90) REVERT: H 83 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.8014 (mtt90) REVERT: H 100 ASP cc_start: 0.8265 (m-30) cc_final: 0.7809 (m-30) REVERT: M 127 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7873 (mt-10) REVERT: M 149 THR cc_start: 0.9202 (t) cc_final: 0.8975 (t) REVERT: M 360 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8669 (m) outliers start: 26 outliers final: 16 residues processed: 217 average time/residue: 0.2446 time to fit residues: 81.5273 Evaluate side-chains 177 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 360 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 overall best weight: 7.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN G 116 ASN M 109 GLN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 HIS ** M 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16172 Z= 0.367 Angle : 0.669 7.534 23100 Z= 0.355 Chirality : 0.044 0.331 2871 Planarity : 0.005 0.045 2074 Dihedral : 23.140 178.017 5119 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.84 % Allowed : 12.58 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1324 helix: -1.62 (0.25), residues: 325 sheet: -0.18 (0.24), residues: 449 loop : -1.55 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 32 HIS 0.006 0.002 HIS M 55 PHE 0.029 0.003 PHE M 105 TYR 0.023 0.002 TYR F 58 ARG 0.007 0.001 ARG M 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.274 Fit side-chains REVERT: A 88 MET cc_start: 0.8323 (ptp) cc_final: 0.6563 (mmt) REVERT: A 106 LYS cc_start: 0.8826 (mttm) cc_final: 0.7319 (tmtt) REVERT: F 12 ASN cc_start: 0.7797 (m-40) cc_final: 0.7392 (t0) REVERT: F 33 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8079 (pp) REVERT: G 38 ARG cc_start: 0.8462 (tpm-80) cc_final: 0.6458 (ptt-90) REVERT: H 100 ASP cc_start: 0.8307 (m-30) cc_final: 0.7881 (m-30) REVERT: M 388 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8192 (ttm110) outliers start: 43 outliers final: 30 residues processed: 198 average time/residue: 0.2230 time to fit residues: 69.5241 Evaluate side-chains 183 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 3 ASN C 36 ASN M 211 GLN M 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16172 Z= 0.270 Angle : 0.600 7.160 23100 Z= 0.319 Chirality : 0.042 0.359 2871 Planarity : 0.004 0.042 2074 Dihedral : 22.721 179.794 5119 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.48 % Allowed : 14.27 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1324 helix: -1.02 (0.27), residues: 323 sheet: 0.04 (0.24), residues: 448 loop : -1.38 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 32 HIS 0.004 0.001 HIS M 55 PHE 0.020 0.002 PHE H 4 TYR 0.014 0.002 TYR B 42 ARG 0.004 0.001 ARG M 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.333 Fit side-chains REVERT: A 88 MET cc_start: 0.8251 (ptp) cc_final: 0.6467 (mmt) REVERT: A 106 LYS cc_start: 0.8889 (mttm) cc_final: 0.7331 (tmtt) REVERT: E 128 ILE cc_start: 0.9007 (mm) cc_final: 0.8636 (mm) REVERT: F 12 ASN cc_start: 0.7744 (m-40) cc_final: 0.7368 (t0) REVERT: F 33 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (pp) REVERT: G 38 ARG cc_start: 0.8515 (tpm-80) cc_final: 0.6418 (ptt-90) REVERT: H 100 ASP cc_start: 0.8289 (m-30) cc_final: 0.7888 (m-30) outliers start: 39 outliers final: 29 residues processed: 190 average time/residue: 0.2395 time to fit residues: 70.0804 Evaluate side-chains 184 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 3 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16172 Z= 0.372 Angle : 0.656 7.983 23100 Z= 0.345 Chirality : 0.044 0.318 2871 Planarity : 0.005 0.045 2074 Dihedral : 22.596 178.132 5119 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.46 % Allowed : 13.92 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1324 helix: -0.91 (0.27), residues: 324 sheet: 0.09 (0.24), residues: 431 loop : -1.34 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 32 HIS 0.006 0.002 HIS M 55 PHE 0.019 0.002 PHE C 4 TYR 0.018 0.002 TYR A 58 ARG 0.005 0.001 ARG M 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.353 Fit side-chains REVERT: A 48 VAL cc_start: 0.9210 (t) cc_final: 0.8948 (p) REVERT: A 88 MET cc_start: 0.8420 (ptp) cc_final: 0.6684 (mmt) REVERT: A 106 LYS cc_start: 0.8940 (mttm) cc_final: 0.7264 (tmtt) REVERT: F 12 ASN cc_start: 0.8001 (m-40) cc_final: 0.7470 (t0) REVERT: F 33 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8071 (pp) REVERT: G 38 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.6462 (ptt-90) REVERT: H 100 ASP cc_start: 0.8283 (m-30) cc_final: 0.7847 (m-30) REVERT: M 228 MET cc_start: 0.8946 (mtm) cc_final: 0.8638 (mtm) REVERT: M 388 ARG cc_start: 0.8534 (mtt180) cc_final: 0.8226 (ttm110) outliers start: 50 outliers final: 37 residues processed: 196 average time/residue: 0.2200 time to fit residues: 68.0893 Evaluate side-chains 196 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 325 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 147 optimal weight: 40.0000 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN C 36 ASN D 6 GLN E 50 GLN H 27 ASN H 87 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16172 Z= 0.338 Angle : 0.620 7.710 23100 Z= 0.324 Chirality : 0.043 0.314 2871 Planarity : 0.005 0.044 2074 Dihedral : 22.407 177.576 5119 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.73 % Allowed : 14.54 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1324 helix: -0.72 (0.28), residues: 323 sheet: 0.26 (0.25), residues: 437 loop : -1.35 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 32 HIS 0.005 0.001 HIS M 55 PHE 0.018 0.002 PHE H 4 TYR 0.019 0.002 TYR E 129 ARG 0.005 0.001 ARG H 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 163 time to evaluate : 1.263 Fit side-chains REVERT: A 88 MET cc_start: 0.8283 (ptp) cc_final: 0.6564 (mmt) REVERT: A 106 LYS cc_start: 0.8934 (mttm) cc_final: 0.7371 (tmtt) REVERT: F 12 ASN cc_start: 0.8013 (m-40) cc_final: 0.7478 (t0) REVERT: F 33 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8012 (pp) REVERT: G 11 ASP cc_start: 0.9029 (t0) cc_final: 0.8804 (t0) REVERT: G 38 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.6528 (ptt-90) REVERT: H 76 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8223 (mm-30) REVERT: H 100 ASP cc_start: 0.8230 (m-30) cc_final: 0.7804 (m-30) REVERT: M 228 MET cc_start: 0.8956 (mtm) cc_final: 0.8701 (mtm) REVERT: M 388 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8241 (ttm110) outliers start: 53 outliers final: 42 residues processed: 195 average time/residue: 0.2268 time to fit residues: 69.3171 Evaluate side-chains 201 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN E 50 GLN G 40 GLN H 87 ASN M 45 ASN M 211 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16172 Z= 0.174 Angle : 0.519 6.619 23100 Z= 0.272 Chirality : 0.039 0.303 2871 Planarity : 0.004 0.040 2074 Dihedral : 22.134 178.842 5119 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.57 % Allowed : 15.97 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1324 helix: -0.22 (0.29), residues: 323 sheet: 0.60 (0.26), residues: 428 loop : -1.16 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 32 HIS 0.002 0.001 HIS M 55 PHE 0.017 0.002 PHE H 4 TYR 0.015 0.001 TYR E 129 ARG 0.006 0.000 ARG H 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 1.247 Fit side-chains REVERT: A 88 MET cc_start: 0.8220 (ptp) cc_final: 0.6509 (mmt) REVERT: A 106 LYS cc_start: 0.8980 (mttm) cc_final: 0.7360 (tmtt) REVERT: B 15 THR cc_start: 0.8422 (t) cc_final: 0.8112 (m) REVERT: C 69 THR cc_start: 0.9116 (m) cc_final: 0.8910 (t) REVERT: E 29 VAL cc_start: 0.9444 (t) cc_final: 0.9080 (m) REVERT: F 12 ASN cc_start: 0.7873 (m-40) cc_final: 0.7363 (t0) REVERT: F 33 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7979 (pp) REVERT: F 56 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7805 (ttm170) REVERT: F 128 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6609 (mp) REVERT: G 38 ARG cc_start: 0.8560 (tpm-80) cc_final: 0.6500 (ptt90) REVERT: H 100 ASP cc_start: 0.8171 (m-30) cc_final: 0.7810 (m-30) REVERT: M 388 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8152 (ttm110) outliers start: 40 outliers final: 28 residues processed: 199 average time/residue: 0.2263 time to fit residues: 69.8291 Evaluate side-chains 195 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16172 Z= 0.394 Angle : 0.642 7.176 23100 Z= 0.335 Chirality : 0.043 0.323 2871 Planarity : 0.005 0.044 2074 Dihedral : 22.281 178.049 5119 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.93 % Allowed : 15.70 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1324 helix: -0.51 (0.28), residues: 323 sheet: 0.41 (0.26), residues: 402 loop : -1.27 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 32 HIS 0.006 0.001 HIS M 55 PHE 0.017 0.002 PHE B 7 TYR 0.020 0.002 TYR E 129 ARG 0.007 0.001 ARG H 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 1.362 Fit side-chains REVERT: A 88 MET cc_start: 0.8343 (ptp) cc_final: 0.6599 (mmt) REVERT: A 106 LYS cc_start: 0.8967 (mttm) cc_final: 0.7369 (tmtt) REVERT: B 6 GLN cc_start: 0.8778 (pt0) cc_final: 0.8539 (pt0) REVERT: B 15 THR cc_start: 0.8505 (t) cc_final: 0.8206 (m) REVERT: F 12 ASN cc_start: 0.7955 (m-40) cc_final: 0.7400 (t0) REVERT: F 33 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8032 (pp) REVERT: G 38 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.6568 (ptt-90) REVERT: H 76 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8199 (mm-30) REVERT: H 100 ASP cc_start: 0.8203 (m-30) cc_final: 0.7784 (m-30) REVERT: M 388 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8263 (ttm110) outliers start: 44 outliers final: 35 residues processed: 182 average time/residue: 0.2314 time to fit residues: 65.7459 Evaluate side-chains 191 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN E 50 GLN H 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16172 Z= 0.249 Angle : 0.560 6.221 23100 Z= 0.293 Chirality : 0.041 0.311 2871 Planarity : 0.004 0.042 2074 Dihedral : 22.109 177.740 5119 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.30 % Allowed : 16.32 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1324 helix: -0.24 (0.29), residues: 323 sheet: 0.50 (0.26), residues: 402 loop : -1.19 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 32 HIS 0.003 0.001 HIS M 55 PHE 0.016 0.002 PHE H 4 TYR 0.016 0.002 TYR E 129 ARG 0.003 0.000 ARG M 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 1.263 Fit side-chains REVERT: A 88 MET cc_start: 0.8250 (ptp) cc_final: 0.6418 (mmt) REVERT: A 106 LYS cc_start: 0.8995 (mttm) cc_final: 0.7384 (tmtt) REVERT: B 6 GLN cc_start: 0.8745 (pt0) cc_final: 0.8533 (pt0) REVERT: B 15 THR cc_start: 0.8459 (t) cc_final: 0.8151 (m) REVERT: E 29 VAL cc_start: 0.9506 (t) cc_final: 0.9175 (m) REVERT: F 33 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8007 (pp) REVERT: F 56 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7835 (ttm170) REVERT: G 38 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6557 (ptt-90) REVERT: H 100 ASP cc_start: 0.8213 (m-30) cc_final: 0.7805 (m-30) REVERT: M 388 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8202 (ttm110) outliers start: 37 outliers final: 34 residues processed: 181 average time/residue: 0.2308 time to fit residues: 64.6319 Evaluate side-chains 190 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 0.0270 chunk 128 optimal weight: 20.0000 overall best weight: 2.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN H 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16172 Z= 0.161 Angle : 0.513 6.139 23100 Z= 0.270 Chirality : 0.039 0.301 2871 Planarity : 0.004 0.041 2074 Dihedral : 21.980 178.948 5119 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.85 % Allowed : 16.95 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1324 helix: 0.09 (0.29), residues: 323 sheet: 0.73 (0.26), residues: 402 loop : -1.08 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 32 HIS 0.002 0.001 HIS M 55 PHE 0.025 0.002 PHE M 265 TYR 0.014 0.001 TYR E 129 ARG 0.004 0.000 ARG H 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.314 Fit side-chains REVERT: A 88 MET cc_start: 0.8161 (ptp) cc_final: 0.6525 (mmt) REVERT: A 106 LYS cc_start: 0.8975 (mttm) cc_final: 0.7376 (tmtt) REVERT: B 6 GLN cc_start: 0.8686 (pt0) cc_final: 0.8451 (pt0) REVERT: B 15 THR cc_start: 0.8404 (t) cc_final: 0.8079 (m) REVERT: E 29 VAL cc_start: 0.9456 (t) cc_final: 0.9140 (m) REVERT: F 12 ASN cc_start: 0.7828 (m-40) cc_final: 0.7313 (t0) REVERT: F 56 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7834 (ttm170) REVERT: G 38 ARG cc_start: 0.8565 (tpm-80) cc_final: 0.6485 (ptt-90) REVERT: H 100 ASP cc_start: 0.8177 (m-30) cc_final: 0.7822 (m-30) REVERT: M 216 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8269 (ttt) REVERT: M 388 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8134 (ttm110) outliers start: 32 outliers final: 28 residues processed: 191 average time/residue: 0.2468 time to fit residues: 72.6108 Evaluate side-chains 196 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 17 optimal weight: 0.0170 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN F 109 GLN H 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099094 restraints weight = 28686.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100785 restraints weight = 15284.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101454 restraints weight = 10995.887| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16172 Z= 0.209 Angle : 0.531 7.896 23100 Z= 0.278 Chirality : 0.040 0.309 2871 Planarity : 0.004 0.042 2074 Dihedral : 21.970 178.723 5119 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.94 % Allowed : 17.31 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1324 helix: 0.14 (0.29), residues: 323 sheet: 0.76 (0.26), residues: 402 loop : -1.06 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 32 HIS 0.003 0.001 HIS M 55 PHE 0.014 0.002 PHE H 4 TYR 0.015 0.001 TYR E 129 ARG 0.003 0.000 ARG H 56 =============================================================================== Job complete usr+sys time: 2722.47 seconds wall clock time: 49 minutes 39.54 seconds (2979.54 seconds total)