Starting phenix.real_space_refine on Sat Jan 20 13:35:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/01_2024/5tc1_8397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/01_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_8397/01_2024/5tc1_8397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/01_2024/5tc1_8397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/01_2024/5tc1_8397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/01_2024/5tc1_8397.pdb" } 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 Residue "M ARG 2": "NH1" <-> "NH2" Residue "M ARG 9": "NH1" <-> "NH2" Residue "M ARG 43": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ARG 147": "NH1" <-> "NH2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "M ARG 177": "NH1" <-> "NH2" Residue "M ARG 188": "NH1" <-> "NH2" Residue "M ARG 229": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 358": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 8.65, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 7.31 Conformation dependent library (CDL) restraints added in 1.9 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: 5.73 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: 5.03 Time building geometry restraints manager: 7.79 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: 97.86 - 106.34: 1551 106.34 - 114.83: 10158 114.83 - 123.31: 9862 123.31 - 131.79: 1429 131.79 - 140.27: 100 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: 8995 35.56 - 71.12: 560 71.12 - 106.68: 89 106.68 - 142.24: 3 142.24 - 177.80: 14 Dihedral angle restraints: 9661 sinusoidal: 5758 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 9658 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 2.520 nonbonded pdb=" OG SER M 58 " pdb=" O6 G R3555 " model vdw 1.430 2.440 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 2.520 ... (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 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: 1.780 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: 7.380 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 46.700 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.080 ------------------------------------------------------------------------------- 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 : 21.286 177.798 7139 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 : 1.380 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: 0.2664 time to fit residues: 130.2240 Evaluate side-chains 210 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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: 9.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN B 3 ASN B 116 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 36 ASN D 116 ASN F 6 GLN F 116 ASN G 54 GLN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 352 GLN M 357 HIS M 389 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2808 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= 0.261 Angle : 0.672 8.081 23100 Z= 0.354 Chirality : 0.043 0.267 2871 Planarity : 0.005 0.049 2074 Dihedral : 22.821 179.037 4851 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.50 % Allowed : 10.88 % Favored : 86.62 % 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: -2.48 (0.21), residues: 1324 helix: -2.74 (0.20), residues: 325 sheet: -0.35 (0.24), residues: 436 loop : -1.90 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 32 HIS 0.002 0.001 HIS M 221 PHE 0.027 0.003 PHE M 105 TYR 0.014 0.002 TYR F 58 ARG 0.007 0.001 ARG M 123 *********************** 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 234 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 206 time to evaluate : 1.340 Fit side-chains REVERT: A 88 MET cc_start: 0.8269 (ptp) cc_final: 0.6416 (mmt) REVERT: A 106 LYS cc_start: 0.8733 (mttm) cc_final: 0.7220 (tmtt) REVERT: E 128 ILE cc_start: 0.8920 (mm) cc_final: 0.8454 (mm) REVERT: F 12 ASN cc_start: 0.7796 (m-40) cc_final: 0.7498 (t0) REVERT: F 33 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8076 (pp) REVERT: F 56 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7364 (mtp180) REVERT: G 38 ARG cc_start: 0.8172 (tpm-80) cc_final: 0.6464 (ptt-90) REVERT: H 100 ASP cc_start: 0.8259 (m-30) cc_final: 0.7801 (m-30) REVERT: M 149 THR cc_start: 0.9201 (t) cc_final: 0.8997 (t) outliers start: 28 outliers final: 22 residues processed: 227 average time/residue: 0.2423 time to fit residues: 84.5101 Evaluate side-chains 189 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 19 THR 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 5 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain E residue 5 THR 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 294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 D 116 ASN E 116 ASN M 109 GLN M 221 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16172 Z= 0.362 Angle : 0.659 7.250 23100 Z= 0.350 Chirality : 0.044 0.334 2871 Planarity : 0.005 0.046 2074 Dihedral : 22.280 177.845 4851 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.73 % Allowed : 11.78 % Favored : 83.50 % 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: -1.71 (0.22), residues: 1324 helix: -1.48 (0.25), residues: 325 sheet: -0.18 (0.24), residues: 441 loop : -1.60 (0.25), residues: 558 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 0.028 0.003 PHE M 105 TYR 0.021 0.002 TYR F 58 ARG 0.005 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 223 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.251 Fit side-chains REVERT: A 88 MET cc_start: 0.8380 (ptp) cc_final: 0.6660 (mmt) REVERT: A 106 LYS cc_start: 0.8842 (mttm) cc_final: 0.7332 (tmtt) REVERT: E 128 ILE cc_start: 0.8984 (mm) cc_final: 0.8608 (mm) REVERT: F 12 ASN cc_start: 0.7801 (m-40) cc_final: 0.7426 (t0) REVERT: F 33 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8051 (pp) REVERT: G 38 ARG cc_start: 0.8511 (tpm-80) cc_final: 0.6496 (ptt-90) REVERT: H 100 ASP cc_start: 0.8297 (m-30) cc_final: 0.7870 (m-30) REVERT: M 253 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7993 (p) outliers start: 53 outliers final: 36 residues processed: 207 average time/residue: 0.2200 time to fit residues: 71.8976 Evaluate side-chains 194 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 ASN 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 5 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 5 THR 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 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN 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 231 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 294 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 0.0770 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: 5.9990 overall best weight: 5.8146 ------------------------------------------------------------------------------- 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 36 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3836 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= 0.283 Angle : 0.592 7.880 23100 Z= 0.310 Chirality : 0.041 0.318 2871 Planarity : 0.004 0.041 2074 Dihedral : 21.743 178.007 4851 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.66 % Allowed : 14.09 % 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: -1.30 (0.22), residues: 1324 helix: -0.98 (0.27), residues: 324 sheet: 0.10 (0.24), residues: 448 loop : -1.53 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 32 HIS 0.004 0.001 HIS M 55 PHE 0.017 0.002 PHE M 105 TYR 0.015 0.002 TYR B 42 ARG 0.003 0.001 ARG M 185 *********************** 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: 41 poor density : 162 time to evaluate : 1.395 Fit side-chains REVERT: A 88 MET cc_start: 0.8334 (ptp) cc_final: 0.6562 (mmt) REVERT: A 106 LYS cc_start: 0.8943 (mttm) cc_final: 0.7251 (tmtt) REVERT: C 38 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7649 (tpt-90) REVERT: E 128 ILE cc_start: 0.8986 (mm) cc_final: 0.8639 (mm) REVERT: F 12 ASN cc_start: 0.7760 (m-40) cc_final: 0.7406 (t0) REVERT: F 33 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8012 (pp) REVERT: G 38 ARG cc_start: 0.8505 (tpm-80) cc_final: 0.6427 (ptt-90) REVERT: H 100 ASP cc_start: 0.8284 (m-30) cc_final: 0.7885 (m-30) outliers start: 41 outliers final: 30 residues processed: 188 average time/residue: 0.2352 time to fit residues: 68.6976 Evaluate side-chains 185 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 17 ASP 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 114 ASP Chi-restraints excluded: chain F residue 129 TYR 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 155 THR Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 294 SER 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: 8.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- 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 D 116 ASN E 50 GLN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 GLN ** M 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16172 Z= 0.232 Angle : 0.549 6.771 23100 Z= 0.287 Chirality : 0.040 0.313 2871 Planarity : 0.004 0.040 2074 Dihedral : 21.568 177.735 4851 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.55 % Allowed : 14.09 % Favored : 81.36 % 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: -0.94 (0.23), residues: 1324 helix: -0.58 (0.28), residues: 324 sheet: 0.31 (0.25), residues: 422 loop : -1.29 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 32 HIS 0.003 0.001 HIS M 55 PHE 0.014 0.002 PHE H 4 TYR 0.015 0.001 TYR B 42 ARG 0.004 0.000 ARG H 56 *********************** 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 217 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 1.491 Fit side-chains REVERT: A 88 MET cc_start: 0.8296 (ptp) cc_final: 0.6555 (mmt) REVERT: A 106 LYS cc_start: 0.8929 (mttm) cc_final: 0.7340 (tmtt) REVERT: C 38 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7532 (tpt-90) REVERT: E 128 ILE cc_start: 0.8980 (mm) cc_final: 0.8657 (mm) REVERT: F 12 ASN cc_start: 0.7823 (m-40) cc_final: 0.7389 (t0) REVERT: F 33 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8040 (pp) REVERT: G 38 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.6480 (ptt-90) REVERT: H 76 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8182 (mm-30) REVERT: H 100 ASP cc_start: 0.8196 (m-30) cc_final: 0.7793 (m-30) REVERT: M 182 ASN cc_start: 0.7274 (OUTLIER) cc_final: 0.6944 (p0) REVERT: M 228 MET cc_start: 0.8928 (mtm) cc_final: 0.8642 (mtm) REVERT: M 253 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8040 (p) outliers start: 51 outliers final: 34 residues processed: 199 average time/residue: 0.2256 time to fit residues: 70.7719 Evaluate side-chains 198 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 6 GLN 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 5 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 17 ASP 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 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 141 VAL Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 294 SER Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 147 optimal weight: 40.0000 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** A 116 ASN C 36 ASN D 116 ASN E 50 GLN M 211 GLN M 282 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16172 Z= 0.361 Angle : 0.631 7.770 23100 Z= 0.330 Chirality : 0.043 0.324 2871 Planarity : 0.005 0.044 2074 Dihedral : 21.663 177.681 4851 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.00 % Allowed : 14.45 % Favored : 80.55 % 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: -0.69 (0.28), residues: 324 sheet: 0.33 (0.25), residues: 417 loop : -1.37 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 32 HIS 0.006 0.001 HIS M 55 PHE 0.016 0.002 PHE M 105 TYR 0.014 0.002 TYR B 42 ARG 0.004 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 218 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 162 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 88 MET cc_start: 0.8363 (ptp) cc_final: 0.6622 (mmt) REVERT: A 106 LYS cc_start: 0.8955 (mttm) cc_final: 0.7373 (tmtt) REVERT: C 38 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7682 (tpt-90) REVERT: E 128 ILE cc_start: 0.9020 (mm) cc_final: 0.8635 (mm) REVERT: F 12 ASN cc_start: 0.7942 (m-40) cc_final: 0.7483 (t0) REVERT: F 33 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8049 (pp) REVERT: F 128 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6853 (mp) REVERT: G 38 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.6613 (ptt90) REVERT: H 100 ASP cc_start: 0.8201 (m-30) cc_final: 0.7765 (m-30) REVERT: M 182 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7102 (p0) REVERT: M 253 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8114 (p) outliers start: 56 outliers final: 44 residues processed: 199 average time/residue: 0.2301 time to fit residues: 70.9472 Evaluate side-chains 208 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 158 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 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 6 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 ASN 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 5 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 38 ARG Chi-restraints excluded: chain C residue 52 SER 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 17 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 5 THR 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 114 ASP 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 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 141 VAL Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 294 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 90 optimal weight: 0.1980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN C 36 ASN D 116 ASN E 50 GLN G 40 GLN H 87 ASN M 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16172 Z= 0.132 Angle : 0.493 6.134 23100 Z= 0.259 Chirality : 0.038 0.300 2871 Planarity : 0.004 0.038 2074 Dihedral : 21.276 179.288 4851 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.12 % Allowed : 16.59 % Favored : 80.29 % 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: -0.48 (0.23), residues: 1324 helix: -0.02 (0.29), residues: 324 sheet: 0.62 (0.26), residues: 410 loop : -1.14 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 32 HIS 0.001 0.000 HIS M 357 PHE 0.014 0.001 PHE H 4 TYR 0.014 0.001 TYR B 42 ARG 0.003 0.000 ARG E 38 *********************** 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 219 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.250 Fit side-chains REVERT: A 88 MET cc_start: 0.8207 (ptp) cc_final: 0.6568 (mmt) REVERT: A 106 LYS cc_start: 0.8989 (mttm) cc_final: 0.7333 (tmtt) REVERT: B 89 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6897 (mt-10) REVERT: C 69 THR cc_start: 0.9127 (m) cc_final: 0.8832 (p) REVERT: E 24 ASN cc_start: 0.8101 (t0) cc_final: 0.7721 (t0) REVERT: E 128 ILE cc_start: 0.8955 (mm) cc_final: 0.8601 (mm) REVERT: F 12 ASN cc_start: 0.7897 (m-40) cc_final: 0.7313 (t0) REVERT: F 56 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7763 (ttm170) REVERT: F 128 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6685 (mp) REVERT: G 38 ARG cc_start: 0.8462 (tpm-80) cc_final: 0.6500 (ptt-90) REVERT: H 56 ARG cc_start: 0.8627 (mtp85) cc_final: 0.7657 (mtt180) REVERT: M 182 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7001 (p0) outliers start: 35 outliers final: 27 residues processed: 207 average time/residue: 0.2393 time to fit residues: 76.4138 Evaluate side-chains 195 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 C residue 5 THR 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 17 ASP 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 33 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 294 SER 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: 9.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 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 6 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 116 ASN E 109 GLN H 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16172 Z= 0.366 Angle : 0.622 8.393 23100 Z= 0.322 Chirality : 0.042 0.318 2871 Planarity : 0.005 0.043 2074 Dihedral : 21.439 177.479 4851 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.46 % Allowed : 15.34 % 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: -0.76 (0.23), residues: 1324 helix: -0.35 (0.28), residues: 324 sheet: 0.52 (0.26), residues: 416 loop : -1.32 (0.25), residues: 584 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 0.016 0.002 PHE D 7 TYR 0.014 0.002 TYR B 42 ARG 0.004 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 203 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 153 time to evaluate : 1.263 Fit side-chains REVERT: A 88 MET cc_start: 0.8319 (ptp) cc_final: 0.6654 (mmt) REVERT: A 106 LYS cc_start: 0.8969 (mttm) cc_final: 0.7383 (tmtt) REVERT: C 38 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7478 (tpt-90) REVERT: E 128 ILE cc_start: 0.9029 (mm) cc_final: 0.8668 (mm) REVERT: F 12 ASN cc_start: 0.7864 (m-40) cc_final: 0.7369 (t0) REVERT: F 33 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8075 (pp) REVERT: G 38 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.6557 (ptt-90) REVERT: H 35 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8869 (p) REVERT: H 100 ASP cc_start: 0.8207 (m-30) cc_final: 0.7775 (m-30) REVERT: M 182 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7098 (p0) outliers start: 50 outliers final: 36 residues processed: 186 average time/residue: 0.2263 time to fit residues: 65.4350 Evaluate side-chains 193 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL 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 C residue 5 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 38 ARG Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 17 ASP 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 71 THR Chi-restraints excluded: chain F residue 17 ASP 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 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 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 141 VAL Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 294 SER 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: 0.0870 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 40.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- 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 C 36 ASN H 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4504 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= 0.240 Angle : 0.552 9.562 23100 Z= 0.284 Chirality : 0.040 0.316 2871 Planarity : 0.004 0.041 2074 Dihedral : 21.282 177.856 4851 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.75 % Allowed : 16.41 % Favored : 79.84 % 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: -0.59 (0.23), residues: 1324 helix: -0.11 (0.29), residues: 324 sheet: 0.59 (0.26), residues: 416 loop : -1.26 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 32 HIS 0.003 0.001 HIS M 55 PHE 0.014 0.002 PHE H 4 TYR 0.015 0.001 TYR B 42 ARG 0.005 0.000 ARG H 56 *********************** 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 207 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 1.339 Fit side-chains REVERT: A 88 MET cc_start: 0.8296 (ptp) cc_final: 0.6562 (mmt) REVERT: A 106 LYS cc_start: 0.9005 (mttm) cc_final: 0.7412 (tmtt) REVERT: C 38 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7456 (tpt-90) REVERT: C 69 THR cc_start: 0.9093 (m) cc_final: 0.8863 (p) REVERT: E 128 ILE cc_start: 0.9016 (mm) cc_final: 0.8651 (mm) REVERT: F 12 ASN cc_start: 0.7872 (m-40) cc_final: 0.7353 (t0) REVERT: F 33 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8083 (pp) REVERT: F 56 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.7794 (ttm170) REVERT: F 128 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6708 (mp) REVERT: G 38 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6521 (ptt-90) REVERT: H 56 ARG cc_start: 0.8647 (mtp85) cc_final: 0.7769 (mtt180) REVERT: H 100 ASP cc_start: 0.8188 (m-30) cc_final: 0.7790 (m-30) REVERT: M 182 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7060 (p0) outliers start: 42 outliers final: 34 residues processed: 192 average time/residue: 0.2358 time to fit residues: 69.9730 Evaluate side-chains 199 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 87 ASN 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 97 THR Chi-restraints excluded: chain C residue 5 THR 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 38 ARG Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 45 THR 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 71 THR Chi-restraints excluded: chain F residue 17 ASP 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 128 ILE 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 97 THR Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 294 SER 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: 8.9990 chunk 68 optimal weight: 20.0000 chunk 100 optimal weight: 0.0020 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 95 optimal weight: 0.3980 chunk 128 optimal weight: 20.0000 overall best weight: 3.5792 ------------------------------------------------------------------------------- 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** C 36 ASN D 116 ASN H 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16172 Z= 0.197 Angle : 0.524 8.364 23100 Z= 0.271 Chirality : 0.039 0.314 2871 Planarity : 0.004 0.041 2074 Dihedral : 21.215 178.358 4851 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.12 % Allowed : 16.95 % Favored : 79.93 % 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: -0.44 (0.23), residues: 1324 helix: 0.05 (0.29), residues: 324 sheet: 0.74 (0.26), residues: 415 loop : -1.24 (0.26), residues: 585 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 0.022 0.002 PHE M 265 TYR 0.014 0.001 TYR B 42 ARG 0.006 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 197 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.186 Fit side-chains REVERT: A 88 MET cc_start: 0.8210 (ptp) cc_final: 0.6695 (mmt) REVERT: A 106 LYS cc_start: 0.8988 (mttm) cc_final: 0.7385 (tmtt) REVERT: C 38 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7503 (tpt-90) REVERT: C 69 THR cc_start: 0.9113 (m) cc_final: 0.8872 (p) REVERT: E 106 LYS cc_start: 0.8765 (mttp) cc_final: 0.8396 (mtpt) REVERT: E 128 ILE cc_start: 0.8983 (mm) cc_final: 0.8616 (mm) REVERT: F 12 ASN cc_start: 0.7853 (m-40) cc_final: 0.7457 (t0) REVERT: F 33 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8048 (pp) REVERT: F 56 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.7805 (ttm170) REVERT: G 38 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6463 (ptt90) REVERT: H 56 ARG cc_start: 0.8650 (mtp85) cc_final: 0.7747 (mtt180) REVERT: H 100 ASP cc_start: 0.8183 (m-30) cc_final: 0.7806 (m-30) REVERT: M 182 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7059 (p0) outliers start: 35 outliers final: 30 residues processed: 185 average time/residue: 0.2445 time to fit residues: 69.1147 Evaluate side-chains 193 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 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 C residue 5 THR 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 38 ARG Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 17 ASP 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 67 VAL 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 23 SER Chi-restraints excluded: chain H residue 33 ILE 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 182 ASN Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 294 SER 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 36 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 50 optimal weight: 0.0870 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN H 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098665 restraints weight = 28753.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100330 restraints weight = 15395.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100961 restraints weight = 11110.976| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16172 Z= 0.242 Angle : 0.725 59.200 23100 Z= 0.403 Chirality : 0.040 0.316 2871 Planarity : 0.004 0.041 2074 Dihedral : 21.211 178.379 4851 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.57 % Allowed : 16.86 % Favored : 79.57 % 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: -0.43 (0.23), residues: 1324 helix: 0.05 (0.29), residues: 324 sheet: 0.77 (0.26), residues: 415 loop : -1.25 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 32 HIS 0.003 0.001 HIS M 55 PHE 0.019 0.002 PHE M 265 TYR 0.016 0.001 TYR M 214 ARG 0.005 0.000 ARG H 56 =============================================================================== Job complete usr+sys time: 2784.59 seconds wall clock time: 51 minutes 51.98 seconds (3111.98 seconds total)