Starting phenix.real_space_refine on Wed Sep 25 20:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/09_2024/6r6b_4734.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/09_2024/6r6b_4734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/09_2024/6r6b_4734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/09_2024/6r6b_4734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/09_2024/6r6b_4734.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r6b_4734/09_2024/6r6b_4734.cif" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7703 2.51 5 N 1700 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11416 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 180} Chain breaks: 1 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 2 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1340 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 2 Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1332 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 Chain: "E" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1348 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain breaks: 2 Chain: "F" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1923 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "I" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "G" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "H" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "J" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Time building chain proxies: 7.00, per 1000 atoms: 0.61 Number of scatterers: 11416 At special positions: 0 Unit cell: (92.886, 92.886, 124.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 1939 8.00 N 1700 7.00 C 7703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 78.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.610A pdb=" N PHE A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 78 removed outlier: 3.917A pdb=" N GLY A 54 " --> pdb=" O MET A 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.812A pdb=" N ALA A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.761A pdb=" N ILE A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.561A pdb=" N HIS A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.598A pdb=" N PHE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 159 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.285A pdb=" N ILE A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.909A pdb=" N PHE A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.930A pdb=" N LEU B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 26 through 32 removed outlier: 3.740A pdb=" N PHE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.722A pdb=" N LEU B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Proline residue: B 66 - end of helix removed outlier: 3.883A pdb=" N ALA B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.163A pdb=" N LYS B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.533A pdb=" N ARG B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 174 removed outlier: 3.620A pdb=" N LEU B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix removed outlier: 3.565A pdb=" N VAL B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 4.497A pdb=" N ILE B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Proline residue: B 188 - end of helix removed outlier: 3.769A pdb=" N PHE B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.747A pdb=" N PHE C 30 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 Proline residue: C 66 - end of helix Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.717A pdb=" N LYS C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 removed outlier: 3.712A pdb=" N ARG C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 175 Proline residue: C 160 - end of helix removed outlier: 3.638A pdb=" N VAL C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.653A pdb=" N VAL C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Proline residue: C 188 - end of helix removed outlier: 3.716A pdb=" N PHE C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.530A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 25 removed outlier: 3.513A pdb=" N THR D 25 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 32 removed outlier: 3.642A pdb=" N PHE D 30 " --> pdb=" O CYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 49 through 64 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.631A pdb=" N ALA D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.538A pdb=" N HIS D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.795A pdb=" N ARG D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 175 Proline residue: D 160 - end of helix removed outlier: 3.612A pdb=" N VAL D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 removed outlier: 4.592A pdb=" N ILE D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Proline residue: D 188 - end of helix removed outlier: 3.973A pdb=" N PHE D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 209 Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.522A pdb=" N PHE E 14 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 25 removed outlier: 4.509A pdb=" N ALA E 23 " --> pdb=" O PHE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 41 removed outlier: 3.617A pdb=" N PHE E 30 " --> pdb=" O CYS E 26 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 72 removed outlier: 4.173A pdb=" N LEU E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) Proline residue: E 66 - end of helix Processing helix chain 'E' and resid 97 through 107 removed outlier: 3.723A pdb=" N HIS E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 3.518A pdb=" N ARG E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 175 removed outlier: 3.537A pdb=" N LEU E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 159 " --> pdb=" O PHE E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix removed outlier: 3.500A pdb=" N VAL E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 Proline residue: E 188 - end of helix removed outlier: 3.995A pdb=" N PHE E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 209 removed outlier: 4.141A pdb=" N ALA E 206 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 29 removed outlier: 3.875A pdb=" N ILE F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 17 " --> pdb=" O PHE F 13 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 56 removed outlier: 4.445A pdb=" N ILE F 45 " --> pdb=" O PRO F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.750A pdb=" N SER F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 90 removed outlier: 3.954A pdb=" N PHE F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS F 77 " --> pdb=" O PHE F 73 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.748A pdb=" N SER F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 141 removed outlier: 3.519A pdb=" N ALA F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.531A pdb=" N PHE F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 206 removed outlier: 3.631A pdb=" N ALA F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Proline residue: F 188 - end of helix removed outlier: 3.711A pdb=" N ILE F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL F 192 " --> pdb=" O PRO F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 230 removed outlier: 3.554A pdb=" N ILE F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 222 " --> pdb=" O THR F 218 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 removed outlier: 4.365A pdb=" N GLN F 241 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 35 removed outlier: 3.793A pdb=" N TRP I 21 " --> pdb=" O ILE I 17 " (cutoff:3.500A) Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'I' and resid 48 through 62 removed outlier: 5.383A pdb=" N ILE I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 84 removed outlier: 4.268A pdb=" N LEU I 71 " --> pdb=" O TYR I 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET I 79 " --> pdb=" O CYS I 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 20 removed outlier: 3.636A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 36 Processing helix chain 'G' and resid 48 through 62 removed outlier: 4.512A pdb=" N ILE G 54 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 4.127A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 20 through 35 Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'H' and resid 46 through 62 removed outlier: 4.548A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 82 removed outlier: 4.094A pdb=" N LEU H 71 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 18 Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.568A pdb=" N VAL J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 62 removed outlier: 3.881A pdb=" N GLY J 50 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 54 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 70 through 82 675 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 3.14 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: 3237 1.34 - 1.46: 2874 1.46 - 1.58: 5421 1.58 - 1.70: 1 1.70 - 1.82: 135 Bond restraints: 11668 Sorted by residual: bond pdb=" C LEU A 109 " pdb=" N GLU A 110 " ideal model delta sigma weight residual 1.334 1.467 -0.133 1.61e-02 3.86e+03 6.86e+01 bond pdb=" CA VAL F 67 " pdb=" C VAL F 67 " ideal model delta sigma weight residual 1.523 1.590 -0.067 1.27e-02 6.20e+03 2.78e+01 bond pdb=" C LEU C 159 " pdb=" N PRO C 160 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.73e+01 bond pdb=" N VAL F 67 " pdb=" CA VAL F 67 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.48e+01 bond pdb=" C LEU J 47 " pdb=" N PRO J 48 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 ... (remaining 11663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.46: 15638 5.46 - 10.93: 167 10.93 - 16.39: 7 16.39 - 21.86: 1 21.86 - 27.32: 1 Bond angle restraints: 15814 Sorted by residual: angle pdb=" C VAL F 67 " pdb=" N PHE F 68 " pdb=" CA PHE F 68 " ideal model delta sigma weight residual 126.86 154.18 -27.32 1.57e+00 4.06e-01 3.03e+02 angle pdb=" C SER F 86 " pdb=" CA SER F 86 " pdb=" CB SER F 86 " ideal model delta sigma weight residual 110.67 127.27 -16.60 1.92e+00 2.71e-01 7.47e+01 angle pdb=" N LYS H 83 " pdb=" CA LYS H 83 " pdb=" C LYS H 83 " ideal model delta sigma weight residual 113.38 103.69 9.69 1.23e+00 6.61e-01 6.21e+01 angle pdb=" N SER F 66 " pdb=" CA SER F 66 " pdb=" C SER F 66 " ideal model delta sigma weight residual 108.76 121.99 -13.23 1.69e+00 3.50e-01 6.12e+01 angle pdb=" N ILE C 67 " pdb=" CA ILE C 67 " pdb=" C ILE C 67 " ideal model delta sigma weight residual 112.96 107.06 5.90 1.00e+00 1.00e+00 3.48e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 6090 13.92 - 27.85: 538 27.85 - 41.77: 188 41.77 - 55.70: 36 55.70 - 69.62: 3 Dihedral angle restraints: 6855 sinusoidal: 2640 harmonic: 4215 Sorted by residual: dihedral pdb=" C SER F 86 " pdb=" N SER F 86 " pdb=" CA SER F 86 " pdb=" CB SER F 86 " ideal model delta harmonic sigma weight residual -122.60 -146.11 23.51 0 2.50e+00 1.60e-01 8.84e+01 dihedral pdb=" CA THR G 38 " pdb=" C THR G 38 " pdb=" N VAL G 39 " pdb=" CA VAL G 39 " ideal model delta harmonic sigma weight residual -180.00 -139.00 -41.00 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA GLY I 68 " pdb=" C GLY I 68 " pdb=" N GLU I 69 " pdb=" CA GLU I 69 " ideal model delta harmonic sigma weight residual -180.00 -146.02 -33.98 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 6852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1890 0.166 - 0.332: 36 0.332 - 0.498: 0 0.498 - 0.664: 0 0.664 - 0.830: 1 Chirality restraints: 1927 Sorted by residual: chirality pdb=" CA SER F 86 " pdb=" N SER F 86 " pdb=" C SER F 86 " pdb=" CB SER F 86 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA VAL C 46 " pdb=" N VAL C 46 " pdb=" C VAL C 46 " pdb=" CB VAL C 46 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE G 51 " pdb=" CA ILE G 51 " pdb=" CG1 ILE G 51 " pdb=" CG2 ILE G 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1924 not shown) Planarity restraints: 1877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 109 " -0.033 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C LEU A 109 " 0.106 2.00e-02 2.50e+03 pdb=" O LEU A 109 " -0.039 2.00e-02 2.50e+03 pdb=" N GLU A 110 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 62 " -0.028 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C ASP F 62 " 0.102 2.00e-02 2.50e+03 pdb=" O ASP F 62 " -0.041 2.00e-02 2.50e+03 pdb=" N ILE F 63 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 67 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C VAL F 67 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL F 67 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE F 68 " 0.024 2.00e-02 2.50e+03 ... (remaining 1874 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 30 2.40 - 3.02: 5866 3.02 - 3.65: 17695 3.65 - 4.27: 25556 4.27 - 4.90: 42126 Nonbonded interactions: 91273 Sorted by model distance: nonbonded pdb=" O PHE A 115 " pdb=" OG SER A 137 " model vdw 1.771 3.040 nonbonded pdb=" OE1 GLU B 209 " pdb=" CE LYS H 83 " model vdw 1.812 3.440 nonbonded pdb=" OE1 GLU B 209 " pdb=" CD LYS H 83 " model vdw 1.926 3.440 nonbonded pdb=" OG SER A 134 " pdb=" N LEU A 135 " model vdw 2.120 3.120 nonbonded pdb=" O GLY A 24 " pdb=" OH TYR A 99 " model vdw 2.260 3.040 ... (remaining 91268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 213)) selection = (chain 'B' and (resid 11 through 73 or resid 96 through 116 or resid 133 through \ 213)) selection = (chain 'C' and (resid 11 through 116 or resid 133 through 213)) selection = (chain 'D' and (resid 11 through 116 or resid 133 through 213)) selection = (chain 'E' and (resid 11 through 116 or resid 133 through 213)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.133 11668 Z= 0.644 Angle : 1.362 27.323 15814 Z= 0.693 Chirality : 0.067 0.830 1927 Planarity : 0.009 0.071 1877 Dihedral : 12.493 69.623 4135 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.56 % Favored : 91.09 % Rotamer: Outliers : 1.97 % Allowed : 6.54 % Favored : 91.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.29 % 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: -5.15 (0.17), residues: 1414 helix: -3.10 (0.11), residues: 1064 sheet: None (None), residues: 0 loop : -3.66 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 200 HIS 0.007 0.002 HIS B 106 PHE 0.037 0.003 PHE F 133 TYR 0.024 0.003 TYR D 133 ARG 0.010 0.002 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 531 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7752 (mtpt) REVERT: B 29 LYS cc_start: 0.7992 (tptt) cc_final: 0.7520 (tptm) REVERT: B 172 LEU cc_start: 0.7698 (tt) cc_final: 0.7131 (tt) REVERT: C 175 LEU cc_start: 0.8309 (tp) cc_final: 0.8045 (tt) REVERT: C 177 MET cc_start: 0.6125 (ptp) cc_final: 0.5719 (ptm) REVERT: D 197 LEU cc_start: 0.6869 (tp) cc_final: 0.6582 (tt) REVERT: I 59 SER cc_start: 0.8387 (p) cc_final: 0.8119 (t) REVERT: G 46 THR cc_start: 0.7333 (p) cc_final: 0.7042 (p) REVERT: G 59 SER cc_start: 0.7745 (p) cc_final: 0.7399 (t) outliers start: 25 outliers final: 2 residues processed: 546 average time/residue: 0.2317 time to fit residues: 177.1294 Evaluate side-chains 304 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 21 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 101 GLN F 106 GLN F 156 ASN F 247 HIS ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11668 Z= 0.247 Angle : 0.907 12.932 15814 Z= 0.444 Chirality : 0.046 0.175 1927 Planarity : 0.006 0.059 1877 Dihedral : 6.283 45.503 1518 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 5.12 % Allowed : 19.76 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -3.03 (0.20), residues: 1414 helix: -1.48 (0.14), residues: 1082 sheet: None (None), residues: 0 loop : -3.27 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 200 HIS 0.012 0.001 HIS F 247 PHE 0.024 0.002 PHE F 76 TYR 0.023 0.002 TYR C 27 ARG 0.008 0.001 ARG E 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 365 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.6770 (ppp) cc_final: 0.6556 (ppp) REVERT: D 178 MET cc_start: 0.6811 (ppp) cc_final: 0.5769 (ppp) REVERT: D 179 MET cc_start: 0.7579 (mmm) cc_final: 0.7032 (mpp) REVERT: G 56 VAL cc_start: 0.8172 (m) cc_final: 0.7906 (t) REVERT: G 59 SER cc_start: 0.7788 (p) cc_final: 0.7537 (t) outliers start: 65 outliers final: 21 residues processed: 414 average time/residue: 0.2152 time to fit residues: 129.1164 Evaluate side-chains 318 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 297 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11668 Z= 0.236 Angle : 0.866 11.036 15814 Z= 0.422 Chirality : 0.045 0.197 1927 Planarity : 0.005 0.066 1877 Dihedral : 5.712 44.133 1516 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 4.17 % Allowed : 23.70 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -2.08 (0.22), residues: 1414 helix: -0.78 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -3.02 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 200 HIS 0.002 0.001 HIS E 106 PHE 0.025 0.002 PHE F 76 TYR 0.025 0.002 TYR E 27 ARG 0.007 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 331 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 MET cc_start: 0.7363 (mmm) cc_final: 0.7067 (mmt) REVERT: C 175 LEU cc_start: 0.8454 (tt) cc_final: 0.8148 (tp) REVERT: D 178 MET cc_start: 0.6765 (ppp) cc_final: 0.5765 (ppp) REVERT: D 179 MET cc_start: 0.7605 (mmm) cc_final: 0.7243 (mpp) REVERT: E 177 MET cc_start: 0.7954 (pmm) cc_final: 0.7609 (pmm) REVERT: G 59 SER cc_start: 0.7897 (p) cc_final: 0.7610 (t) outliers start: 53 outliers final: 24 residues processed: 369 average time/residue: 0.2066 time to fit residues: 110.9621 Evaluate side-chains 316 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 292 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 40.0000 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS F 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11668 Z= 0.351 Angle : 0.873 11.747 15814 Z= 0.431 Chirality : 0.046 0.188 1927 Planarity : 0.005 0.061 1877 Dihedral : 5.449 43.951 1516 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 4.80 % Allowed : 24.09 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.40 (0.23), residues: 1414 helix: -0.34 (0.15), residues: 1102 sheet: None (None), residues: 0 loop : -2.72 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 200 HIS 0.004 0.001 HIS E 106 PHE 0.018 0.002 PHE F 249 TYR 0.024 0.002 TYR D 142 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 306 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: C 64 MET cc_start: 0.7411 (mmm) cc_final: 0.7205 (mmt) REVERT: D 179 MET cc_start: 0.7817 (mmm) cc_final: 0.7503 (tpp) REVERT: E 39 ASN cc_start: 0.7592 (m-40) cc_final: 0.7381 (m110) outliers start: 61 outliers final: 31 residues processed: 347 average time/residue: 0.1925 time to fit residues: 99.2951 Evaluate side-chains 305 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 273 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11668 Z= 0.256 Angle : 0.855 9.907 15814 Z= 0.416 Chirality : 0.045 0.191 1927 Planarity : 0.004 0.061 1877 Dihedral : 5.355 45.069 1516 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 3.78 % Allowed : 27.09 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.07 (0.23), residues: 1414 helix: -0.13 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 200 HIS 0.002 0.001 HIS C 106 PHE 0.019 0.001 PHE H 49 TYR 0.033 0.002 TYR A 158 ARG 0.005 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 313 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5588 (mm-30) REVERT: E 39 ASN cc_start: 0.7586 (m-40) cc_final: 0.7291 (m110) REVERT: J 4 ILE cc_start: 0.8369 (mp) cc_final: 0.8105 (pt) outliers start: 48 outliers final: 28 residues processed: 343 average time/residue: 0.1956 time to fit residues: 99.8732 Evaluate side-chains 315 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 287 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain J residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11668 Z= 0.229 Angle : 0.873 13.371 15814 Z= 0.418 Chirality : 0.044 0.197 1927 Planarity : 0.004 0.063 1877 Dihedral : 5.259 45.540 1516 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 3.78 % Allowed : 28.35 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1414 helix: 0.04 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 200 HIS 0.002 0.000 HIS F 70 PHE 0.015 0.001 PHE I 49 TYR 0.027 0.002 TYR D 142 ARG 0.003 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 318 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 52 LYS cc_start: 0.9161 (pttt) cc_final: 0.8950 (ptpp) outliers start: 48 outliers final: 30 residues processed: 347 average time/residue: 0.1941 time to fit residues: 100.5553 Evaluate side-chains 311 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11668 Z= 0.229 Angle : 0.910 14.422 15814 Z= 0.434 Chirality : 0.046 0.232 1927 Planarity : 0.004 0.066 1877 Dihedral : 5.252 45.223 1516 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 3.54 % Allowed : 29.29 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.74 (0.23), residues: 1414 helix: 0.09 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -2.38 (0.42), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 200 HIS 0.002 0.001 HIS F 247 PHE 0.035 0.001 PHE H 49 TYR 0.019 0.001 TYR D 142 ARG 0.002 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 312 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5548 (mm-30) REVERT: B 179 MET cc_start: 0.6633 (tpp) cc_final: 0.6164 (tpp) REVERT: E 26 CYS cc_start: 0.6390 (t) cc_final: 0.6095 (t) REVERT: I 52 LYS cc_start: 0.9137 (pttt) cc_final: 0.8796 (pttm) outliers start: 45 outliers final: 28 residues processed: 341 average time/residue: 0.1871 time to fit residues: 96.1079 Evaluate side-chains 302 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11668 Z= 0.235 Angle : 0.967 17.471 15814 Z= 0.453 Chirality : 0.046 0.304 1927 Planarity : 0.005 0.067 1877 Dihedral : 5.191 46.082 1516 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.68 % Allowed : 30.87 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.78 (0.23), residues: 1414 helix: 0.12 (0.16), residues: 1107 sheet: None (None), residues: 0 loop : -2.61 (0.40), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 PHE 0.023 0.001 PHE H 49 TYR 0.037 0.002 TYR A 158 ARG 0.005 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 295 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 52 LYS cc_start: 0.9138 (pttt) cc_final: 0.8912 (ptpp) outliers start: 34 outliers final: 30 residues processed: 315 average time/residue: 0.2048 time to fit residues: 96.1325 Evaluate side-chains 304 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 274 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain J residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11668 Z= 0.271 Angle : 0.967 14.735 15814 Z= 0.452 Chirality : 0.047 0.316 1927 Planarity : 0.005 0.069 1877 Dihedral : 5.186 45.690 1516 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 2.76 % Allowed : 31.02 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.24), residues: 1414 helix: 0.26 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.68 (0.40), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 PHE 0.027 0.001 PHE H 49 TYR 0.017 0.001 TYR D 142 ARG 0.008 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 MET cc_start: 0.6872 (tpp) cc_final: 0.6531 (mpp) outliers start: 35 outliers final: 30 residues processed: 307 average time/residue: 0.1881 time to fit residues: 87.3592 Evaluate side-chains 301 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 271 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain J residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11668 Z= 0.248 Angle : 0.985 15.438 15814 Z= 0.461 Chirality : 0.046 0.222 1927 Planarity : 0.005 0.070 1877 Dihedral : 5.146 45.262 1516 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 2.60 % Allowed : 31.65 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.61 (0.23), residues: 1414 helix: 0.28 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.84 (0.40), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 200 HIS 0.003 0.001 HIS F 70 PHE 0.030 0.001 PHE H 49 TYR 0.034 0.002 TYR C 27 ARG 0.008 0.001 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 179 MET cc_start: 0.8059 (tpp) cc_final: 0.7686 (tpp) REVERT: H 1 MET cc_start: 0.5991 (tmm) cc_final: 0.5774 (tmm) outliers start: 33 outliers final: 28 residues processed: 308 average time/residue: 0.1898 time to fit residues: 88.6152 Evaluate side-chains 303 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 275 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 75 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050729 restraints weight = 49202.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052358 restraints weight = 27061.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053555 restraints weight = 18534.363| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11668 Z= 0.236 Angle : 0.996 15.618 15814 Z= 0.463 Chirality : 0.046 0.222 1927 Planarity : 0.005 0.072 1877 Dihedral : 5.168 44.975 1516 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 2.83 % Allowed : 31.50 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1414 helix: 0.27 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.76 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 200 HIS 0.004 0.001 HIS F 70 PHE 0.028 0.001 PHE H 49 TYR 0.036 0.001 TYR A 142 ARG 0.007 0.001 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.40 seconds wall clock time: 47 minutes 47.58 seconds (2867.58 seconds total)