Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 22:11:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/07_2023/5tc1_8397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/07_2023/5tc1_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_8397/07_2023/5tc1_8397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/07_2023/5tc1_8397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/07_2023/5tc1_8397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tc1_8397/07_2023/5tc1_8397.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 7.77, per 1000 atoms: 0.50 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: 6.78 Conformation dependent library (CDL) restraints added in 1.5 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 26.6% alpha, 40.5% beta 17 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.829A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.603A pdb=" N GLY B 28 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.692A pdb=" N VAL B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.532A pdb=" N ILE B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.847A pdb=" N GLY C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.623A pdb=" N ALA C 41 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 112 removed outlier: 3.554A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.603A pdb=" N LEU D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.514A pdb=" N ALA D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 removed outlier: 3.552A pdb=" N ALA E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.585A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.890A pdb=" N GLY F 28 " --> pdb=" O PHE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 112 removed outlier: 3.687A pdb=" N ILE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 112 " --> pdb=" O MET F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.530A pdb=" N ALA F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 removed outlier: 4.044A pdb=" N GLY G 28 " --> pdb=" O PHE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 removed outlier: 3.573A pdb=" N ALA G 41 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 112 removed outlier: 3.949A pdb=" N LEU G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.623A pdb=" N ALA G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 4.362A pdb=" N GLY H 28 " --> pdb=" O PHE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.590A pdb=" N LEU H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 105 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'M' and resid 98 through 104 removed outlier: 3.696A pdb=" N CYS M 101 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR M 102 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER M 103 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 104 " --> pdb=" O CYS M 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 98 through 104' Processing helix chain 'M' and resid 117 through 135 removed outlier: 4.056A pdb=" N ARG M 123 " --> pdb=" O ASN M 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 131 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR M 133 " --> pdb=" O LEU M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 145 through 150 Processing helix chain 'M' and resid 152 through 169 removed outlier: 3.580A pdb=" N GLN M 156 " --> pdb=" O GLN M 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 166 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 Processing helix chain 'M' and resid 191 through 199 removed outlier: 3.717A pdb=" N LEU M 199 " --> pdb=" O ARG M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 220 Proline residue: M 205 - end of helix removed outlier: 3.663A pdb=" N GLN M 211 " --> pdb=" O MET M 207 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU M 217 " --> pdb=" O ALA M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 224 Processing helix chain 'M' and resid 294 through 300 removed outlier: 3.741A pdb=" N ASP M 298 " --> pdb=" O SER M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 312 removed outlier: 3.503A pdb=" N MET M 306 " --> pdb=" O PRO M 302 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU M 308 " --> pdb=" O GLY M 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR M 311 " --> pdb=" O LEU M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 388 removed outlier: 3.722A pdb=" N ILE M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.710A pdb=" N VAL A 18 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 31 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 61 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG A 56 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 91 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 58 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 89 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 60 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 87 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 62 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 64 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 83 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 66 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 79 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 removed outlier: 7.131A pdb=" N VAL B 18 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ARG D 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL D 72 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN D 70 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA D 80 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA D 68 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP D 82 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 49 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU D 31 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 18 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.891A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 61 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP C 82 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 68 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA C 80 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN C 70 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL C 72 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 7 through 10 removed outlier: 5.262A pdb=" N VAL E 8 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 20 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 10 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU E 31 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 30 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ARG F 83 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 72 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN F 70 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA F 80 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA F 68 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP F 82 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 61 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU F 31 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 18 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 7 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 7 through 10 removed outlier: 5.262A pdb=" N VAL E 8 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 20 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 10 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU E 31 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 30 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ARG E 83 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 61 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU F 31 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 18 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 7 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.858A pdb=" N VAL G 18 " --> pdb=" O LEU G 9 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU G 31 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS G 46 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 61 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG G 49 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 51 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 90 " --> pdb=" O TYR G 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 10 removed outlier: 6.662A pdb=" N VAL H 18 " --> pdb=" O LEU H 9 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLU H 31 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS H 43 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 61 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN H 70 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 38 through 39 removed outlier: 6.745A pdb=" N LYS M 350 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 351 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 327 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TRP M 264 " --> pdb=" O MET M 319 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY M 321 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL M 262 " --> pdb=" O GLY M 321 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL M 323 " --> pdb=" O ARG M 260 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG M 260 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP M 325 " --> pdb=" O SER M 258 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER M 258 " --> pdb=" O ASP M 325 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE M 327 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN M 256 " --> pdb=" O ILE M 327 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY M 329 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR M 254 " --> pdb=" O GLY M 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE M 261 " --> pdb=" O ARG M 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 44 through 45 removed outlier: 4.067A pdb=" N PHE M 44 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER M 61 " --> pdb=" O PHE M 44 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR M 60 " --> pdb=" O ARG M 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 351 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 327 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA M 369 " --> pdb=" O CYS M 316 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 7.18 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: 8702 35.56 - 71.12: 361 71.12 - 106.68: 33 106.68 - 142.24: 3 142.24 - 177.80: 14 Dihedral angle restraints: 9113 sinusoidal: 5210 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 9110 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.460 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.450 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.330 ------------------------------------------------------------------------------- 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 : 18.344 177.798 6591 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 % 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 *********************** 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 : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 335 average time/residue: 0.2703 time to fit residues: 133.0339 Evaluate side-chains 198 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.310 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1684 time to fit residues: 1.9663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 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: 5.1788 ------------------------------------------------------------------------------- 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** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 16172 Z= 0.284 Angle : 0.682 8.420 23100 Z= 0.361 Chirality : 0.044 0.292 2871 Planarity : 0.006 0.049 2074 Dihedral : 18.782 179.467 4301 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 2.85 % 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: -2.46 (0.21), residues: 1324 helix: -2.73 (0.20), residues: 325 sheet: -0.45 (0.24), residues: 441 loop : -1.79 (0.24), residues: 558 *********************** 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 218 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.422 Fit side-chains outliers start: 32 outliers final: 24 residues processed: 211 average time/residue: 0.2303 time to fit residues: 75.0240 Evaluate side-chains 178 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1334 time to fit residues: 7.4577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 overall best weight: 4.6986 ------------------------------------------------------------------------------- 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 E 116 ASN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 GLN M 221 HIS M 252 GLN M 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16172 Z= 0.246 Angle : 0.580 6.574 23100 Z= 0.308 Chirality : 0.041 0.337 2871 Planarity : 0.005 0.045 2074 Dihedral : 17.899 178.798 4301 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.96 % 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: -1.63 (0.22), residues: 1324 helix: -1.45 (0.25), residues: 327 sheet: -0.09 (0.24), residues: 448 loop : -1.59 (0.25), residues: 549 *********************** 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 193 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.383 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 183 average time/residue: 0.2370 time to fit residues: 68.5533 Evaluate side-chains 161 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1397 time to fit residues: 4.4602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 15 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 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: 10.0000 overall best weight: 4.9790 ------------------------------------------------------------------------------- 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 E 50 GLN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 16172 Z= 0.256 Angle : 0.575 8.415 23100 Z= 0.301 Chirality : 0.041 0.338 2871 Planarity : 0.004 0.041 2074 Dihedral : 17.240 178.611 4301 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.78 % 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: -1.16 (0.23), residues: 1324 helix: -0.91 (0.27), residues: 324 sheet: 0.20 (0.24), residues: 448 loop : -1.43 (0.26), residues: 552 *********************** 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 176 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.339 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 166 average time/residue: 0.2242 time to fit residues: 59.1142 Evaluate side-chains 156 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1396 time to fit residues: 3.9962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 GLN E 109 GLN G 6 GLN G 40 GLN ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16172 Z= 0.155 Angle : 0.499 6.572 23100 Z= 0.261 Chirality : 0.038 0.266 2871 Planarity : 0.004 0.037 2074 Dihedral : 16.878 179.375 4301 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.61 % 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: -0.69 (0.23), residues: 1324 helix: -0.36 (0.28), residues: 324 sheet: 0.50 (0.25), residues: 417 loop : -1.16 (0.26), residues: 583 *********************** 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 195 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.326 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 186 average time/residue: 0.2365 time to fit residues: 68.7520 Evaluate side-chains 166 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1326 time to fit residues: 3.6397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 147 optimal weight: 40.0000 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16172 Z= 0.177 Angle : 0.506 8.923 23100 Z= 0.264 Chirality : 0.039 0.329 2871 Planarity : 0.004 0.039 2074 Dihedral : 16.595 179.843 4301 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.16 % 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: -0.40 (0.23), residues: 1324 helix: -0.05 (0.29), residues: 324 sheet: 0.77 (0.25), residues: 429 loop : -1.17 (0.26), residues: 571 *********************** 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 181 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 1.222 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 174 average time/residue: 0.2298 time to fit residues: 62.3045 Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1315 time to fit residues: 3.0061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 overall best weight: 7.2790 ------------------------------------------------------------------------------- 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** D 6 GLN H 116 ASN M 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 16172 Z= 0.344 Angle : 0.601 7.231 23100 Z= 0.315 Chirality : 0.042 0.323 2871 Planarity : 0.004 0.041 2074 Dihedral : 16.742 178.332 4301 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.07 % 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: -0.63 (0.23), residues: 1324 helix: -0.30 (0.28), residues: 324 sheet: 0.62 (0.26), residues: 416 loop : -1.22 (0.25), residues: 584 *********************** 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 166 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.433 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.2434 time to fit residues: 62.1698 Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1508 time to fit residues: 3.4838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN D 116 ASN G 6 GLN H 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 16172 Z= 0.361 Angle : 0.622 7.795 23100 Z= 0.324 Chirality : 0.042 0.312 2871 Planarity : 0.005 0.043 2074 Dihedral : 16.848 178.409 4301 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.43 % 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: -0.79 (0.23), residues: 1324 helix: -0.36 (0.28), residues: 324 sheet: 0.51 (0.25), residues: 431 loop : -1.41 (0.26), residues: 569 *********************** 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 177 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.210 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 169 average time/residue: 0.2343 time to fit residues: 62.2931 Evaluate side-chains 167 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1410 time to fit residues: 4.6505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 144 optimal weight: 30.0000 overall best weight: 7.4110 ------------------------------------------------------------------------------- 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 E 50 GLN H 87 ASN M 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 16172 Z= 0.347 Angle : 0.611 6.853 23100 Z= 0.318 Chirality : 0.042 0.309 2871 Planarity : 0.005 0.043 2074 Dihedral : 16.835 178.111 4301 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.16 % 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: -0.84 (0.23), residues: 1324 helix: -0.31 (0.28), residues: 324 sheet: 0.39 (0.26), residues: 410 loop : -1.35 (0.25), residues: 590 *********************** 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 173 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.251 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 164 average time/residue: 0.2354 time to fit residues: 61.0594 Evaluate side-chains 161 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1440 time to fit residues: 3.9644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 0.0980 chunk 100 optimal weight: 0.0270 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 overall best weight: 2.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** C 6 GLN ** 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: 0.7603 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 16172 Z= 0.151 Angle : 0.495 6.875 23100 Z= 0.257 Chirality : 0.038 0.291 2871 Planarity : 0.004 0.039 2074 Dihedral : 16.474 179.358 4301 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.36 % 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: -0.37 (0.24), residues: 1324 helix: 0.28 (0.29), residues: 324 sheet: 0.70 (0.26), residues: 427 loop : -1.27 (0.26), residues: 573 ********************** 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 176 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.298 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 174 average time/residue: 0.2393 time to fit residues: 64.4519 Evaluate side-chains 169 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1304 time to fit residues: 2.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098138 restraints weight = 28815.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099667 restraints weight = 15916.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100488 restraints weight = 11450.828| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16172 Z= 0.266 Angle : 0.562 7.746 23100 Z= 0.291 Chirality : 0.040 0.343 2871 Planarity : 0.004 0.042 2074 Dihedral : 16.491 179.154 4301 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.45 % 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: -0.49 (0.23), residues: 1324 helix: 0.12 (0.29), residues: 324 sheet: 0.70 (0.26), residues: 402 loop : -1.29 (0.26), residues: 598 =============================================================================== Job complete usr+sys time: 2560.95 seconds wall clock time: 48 minutes 7.65 seconds (2887.65 seconds total)