Starting phenix.real_space_refine on Sun May 3 02:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2t_65579/05_2026/9w2t_65579.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2t_65579/05_2026/9w2t_65579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w2t_65579/05_2026/9w2t_65579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2t_65579/05_2026/9w2t_65579.map" model { file = "/net/cci-nas-00/data/ceres_data/9w2t_65579/05_2026/9w2t_65579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2t_65579/05_2026/9w2t_65579.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 52 5.16 5 C 6629 2.51 5 N 1594 2.21 5 O 1751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 17 Chain: "8" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 330 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1726 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "b" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 367 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain: "e" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 694 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 73} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 275 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 10026 At special positions: 0 Unit cell: (119.173, 113.36, 109, 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 52 16.00 O 1751 8.00 N 1594 7.00 C 6629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 283.6 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 1 sheets defined 84.5% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain '8' and resid 8 through 22 removed outlier: 4.483A pdb=" N MET 8 12 " --> pdb=" O THR 8 8 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE 8 22 " --> pdb=" O LEU 8 18 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 30 removed outlier: 3.978A pdb=" N LYS 8 30 " --> pdb=" O LEU 8 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 15 removed outlier: 5.294A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE K 9 " --> pdb=" O ALA K 5 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY K 12 " --> pdb=" O PHE K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 39 Processing helix chain 'K' and resid 43 through 74 removed outlier: 3.516A pdb=" N SER K 48 " --> pdb=" O GLN K 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR K 49 " --> pdb=" O GLN K 45 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 removed outlier: 3.645A pdb=" N GLY L 12 " --> pdb=" O PHE L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 39 removed outlier: 4.391A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY L 26 " --> pdb=" O GLY L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 71 Processing helix chain 'M' and resid 2 through 15 removed outlier: 4.072A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 39 removed outlier: 4.072A pdb=" N GLY M 22 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 4.523A pdb=" N ALA M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 removed outlier: 4.028A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 39 Processing helix chain 'N' and resid 42 through 74 removed outlier: 3.525A pdb=" N LEU N 46 " --> pdb=" O LEU N 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE N 47 " --> pdb=" O M3L N 43 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER N 48 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR N 49 " --> pdb=" O GLN N 45 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU N 72 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE N 73 " --> pdb=" O PHE N 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 18 through 36 removed outlier: 3.689A pdb=" N GLY O 26 " --> pdb=" O GLY O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 38 No H-bonds generated for 'chain 'O' and resid 37 through 38' Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 42 through 74 removed outlier: 3.784A pdb=" N LEU O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 removed outlier: 4.132A pdb=" N LYS P 7 " --> pdb=" O ASP P 3 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 39 removed outlier: 3.742A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 73 removed outlier: 4.709A pdb=" N SER P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET P 60 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL P 67 " --> pdb=" O PHE P 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA P 68 " --> pdb=" O CYS P 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE P 69 " --> pdb=" O LEU P 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 removed outlier: 3.950A pdb=" N THR Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 39 removed outlier: 4.397A pdb=" N GLY Q 22 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 58 Processing helix chain 'Q' and resid 58 through 73 removed outlier: 4.139A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 16 removed outlier: 3.830A pdb=" N GLY R 12 " --> pdb=" O PHE R 8 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 36 removed outlier: 3.617A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 73 removed outlier: 4.537A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 10 removed outlier: 3.757A pdb=" N PHE a 9 " --> pdb=" O PHE a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 25 removed outlier: 4.036A pdb=" N ILE a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 31 Processing helix chain 'a' and resid 40 through 58 Processing helix chain 'a' and resid 64 through 67 Processing helix chain 'a' and resid 68 through 86 Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 127 Proline residue: a 107 - end of helix removed outlier: 8.006A pdb=" N LYS a 122 " --> pdb=" O ARG a 118 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA a 123 " --> pdb=" O ASN a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 137 Processing helix chain 'a' and resid 138 through 182 removed outlier: 5.433A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 4.026A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR a 161 " --> pdb=" O ALA a 157 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 225 removed outlier: 4.187A pdb=" N ALA a 189 " --> pdb=" O SER a 185 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR a 212 " --> pdb=" O MET a 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 32 through 48 Processing helix chain 'b' and resid 54 through 101 removed outlier: 4.340A pdb=" N PHE b 58 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER b 59 " --> pdb=" O PRO b 55 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 123 Processing helix chain 'd' and resid 126 through 130 Processing helix chain 'd' and resid 131 through 139 Processing helix chain 'd' and resid 140 through 143 Processing helix chain 'e' and resid 7 through 70 removed outlier: 3.787A pdb=" N TYR e 15 " --> pdb=" O LYS e 11 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET e 22 " --> pdb=" O LEU e 18 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA e 23 " --> pdb=" O PHE e 19 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR e 24 " --> pdb=" O LEU e 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY e 25 " --> pdb=" O GLY e 21 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS e 33 " --> pdb=" O TYR e 29 " (cutoff:3.500A) Proline residue: e 34 - end of helix removed outlier: 3.979A pdb=" N GLU e 38 " --> pdb=" O PRO e 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 26 removed outlier: 3.599A pdb=" N ARG f 26 " --> pdb=" O TRP f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 49 Processing helix chain 'f' and resid 55 through 58 removed outlier: 3.854A pdb=" N GLY f 58 " --> pdb=" O SER f 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 55 through 58' Processing helix chain 'f' and resid 59 through 74 removed outlier: 4.431A pdb=" N ALA f 65 " --> pdb=" O MET f 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 82 removed outlier: 3.606A pdb=" N HIS f 80 " --> pdb=" O GLU f 77 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG f 82 " --> pdb=" O LYS f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 37 removed outlier: 4.059A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 61 removed outlier: 4.707A pdb=" N THR g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE g 55 " --> pdb=" O SER g 51 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE g 56 " --> pdb=" O LEU g 52 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR g 61 " --> pdb=" O ASN g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 66 Processing helix chain 'g' and resid 68 through 85 removed outlier: 4.235A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 94 Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.751A pdb=" N LYS j 7 " --> pdb=" O GLN j 3 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 19 removed outlier: 3.510A pdb=" N TYR j 17 " --> pdb=" O MET j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 47 removed outlier: 3.738A pdb=" N TRP j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL j 26 " --> pdb=" O GLN j 22 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG j 44 " --> pdb=" O SER j 40 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER j 45 " --> pdb=" O ALA j 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 22 through 41 removed outlier: 3.717A pdb=" N CYS k 29 " --> pdb=" O GLY k 25 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL k 30 " --> pdb=" O ARG k 26 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL k 41 " --> pdb=" O ILE k 37 " (cutoff:3.500A) Processing helix chain 'k' and resid 41 through 46 Processing sheet with id=AA1, first strand: chain 'b' and resid 12 through 13 761 hydrogen bonds defined for protein. 2238 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: 1.53 Time building geometry restraints manager: 1.27 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: 3035 1.34 - 1.46: 2472 1.46 - 1.58: 4634 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 10235 Sorted by residual: bond pdb=" CA MET a 140 " pdb=" C MET a 140 " ideal model delta sigma weight residual 1.522 1.491 0.030 1.72e-02 3.38e+03 3.12e+00 bond pdb=" CG1 ILE K 34 " pdb=" CD1 ILE K 34 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.80e+00 bond pdb=" C PRO 8 37 " pdb=" N GLU 8 38 " ideal model delta sigma weight residual 1.332 1.314 0.019 1.40e-02 5.10e+03 1.77e+00 bond pdb=" CG GLU Q 58 " pdb=" CD GLU Q 58 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.74e+00 bond pdb=" N GLU Q 58 " pdb=" CA GLU Q 58 " ideal model delta sigma weight residual 1.459 1.471 -0.013 1.25e-02 6.40e+03 1.03e+00 ... (remaining 10230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 13837 5.73 - 11.46: 23 11.46 - 17.19: 1 17.19 - 22.92: 0 22.92 - 28.65: 1 Bond angle restraints: 13862 Sorted by residual: angle pdb=" O M3L L 43 " pdb=" C M3L L 43 " pdb=" N GLN L 44 " ideal model delta sigma weight residual 123.00 94.35 28.65 1.60e+00 3.91e-01 3.21e+02 angle pdb=" O M3L O 43 " pdb=" C M3L O 43 " pdb=" N GLN O 44 " ideal model delta sigma weight residual 123.00 109.04 13.96 1.60e+00 3.91e-01 7.62e+01 angle pdb=" O M3L N 43 " pdb=" C M3L N 43 " pdb=" N GLN N 44 " ideal model delta sigma weight residual 123.00 128.55 -5.55 1.60e+00 3.91e-01 1.20e+01 angle pdb=" N GLU e 57 " pdb=" CA GLU e 57 " pdb=" CB GLU e 57 " ideal model delta sigma weight residual 110.39 115.89 -5.50 1.66e+00 3.63e-01 1.10e+01 angle pdb=" N GLN e 53 " pdb=" CA GLN e 53 " pdb=" CB GLN e 53 " ideal model delta sigma weight residual 110.12 114.98 -4.86 1.47e+00 4.63e-01 1.09e+01 ... (remaining 13857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5372 17.64 - 35.28: 505 35.28 - 52.92: 74 52.92 - 70.56: 13 70.56 - 88.20: 9 Dihedral angle restraints: 5973 sinusoidal: 2248 harmonic: 3725 Sorted by residual: dihedral pdb=" CA MET a 57 " pdb=" C MET a 57 " pdb=" N MET a 58 " pdb=" CA MET a 58 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR g 68 " pdb=" C THR g 68 " pdb=" N VAL g 69 " pdb=" CA VAL g 69 " ideal model delta harmonic sigma weight residual -180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA MET a 58 " pdb=" C MET a 58 " pdb=" N SER a 59 " pdb=" CA SER a 59 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1216 0.045 - 0.090: 331 0.090 - 0.136: 69 0.136 - 0.181: 4 0.181 - 0.226: 2 Chirality restraints: 1622 Sorted by residual: chirality pdb=" CB ILE N 34 " pdb=" CA ILE N 34 " pdb=" CG1 ILE N 34 " pdb=" CG2 ILE N 34 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA GLN a 152 " pdb=" N GLN a 152 " pdb=" C GLN a 152 " pdb=" CB GLN a 152 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA ILE a 184 " pdb=" N ILE a 184 " pdb=" C ILE a 184 " pdb=" CB ILE a 184 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1619 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA M3L L 43 " 0.115 2.00e-02 2.50e+03 1.95e-01 3.81e+02 pdb=" C M3L L 43 " -0.338 2.00e-02 2.50e+03 pdb=" O M3L L 43 " 0.115 2.00e-02 2.50e+03 pdb=" N GLN L 44 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA M3L O 43 " 0.076 2.00e-02 2.50e+03 1.41e-01 2.00e+02 pdb=" C M3L O 43 " -0.245 2.00e-02 2.50e+03 pdb=" O M3L O 43 " 0.087 2.00e-02 2.50e+03 pdb=" N GLN O 44 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA M3L Q 43 " -0.040 2.00e-02 2.50e+03 8.29e-02 6.87e+01 pdb=" C M3L Q 43 " 0.143 2.00e-02 2.50e+03 pdb=" O M3L Q 43 " -0.053 2.00e-02 2.50e+03 pdb=" N GLN Q 44 " -0.050 2.00e-02 2.50e+03 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 3936 2.90 - 3.40: 11815 3.40 - 3.90: 16286 3.90 - 4.40: 17540 4.40 - 4.90: 28211 Nonbonded interactions: 77788 Sorted by model distance: nonbonded pdb=" O GLN e 53 " pdb=" OE1 GLU e 57 " model vdw 2.394 3.040 nonbonded pdb=" O LYS e 49 " pdb=" OE1 GLN e 53 " model vdw 2.426 3.040 nonbonded pdb=" O M3L L 43 " pdb=" CA GLN L 44 " model vdw 2.445 2.776 nonbonded pdb=" O TYR g 32 " pdb=" OE1 GLU g 36 " model vdw 2.493 3.040 nonbonded pdb=" O ARG e 35 " pdb=" OE1 GLU e 39 " model vdw 2.508 3.040 ... (remaining 77783 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 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 7.850 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.004 0.052 10235 Z= 0.163 Angle : 0.784 28.646 13862 Z= 0.407 Chirality : 0.042 0.226 1622 Planarity : 0.008 0.195 1697 Dihedral : 14.105 88.201 3599 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1257 helix: 1.63 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -0.55 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 38 TYR 0.029 0.001 TYR a 221 PHE 0.033 0.002 PHE N 8 TRP 0.028 0.002 TRP d 152 HIS 0.003 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00359 (10235) covalent geometry : angle 0.78434 (13862) hydrogen bonds : bond 0.08957 ( 761) hydrogen bonds : angle 4.10632 ( 2238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.7368 (mm) cc_final: 0.7149 (mm) REVERT: M 7 LYS cc_start: 0.6762 (mttt) cc_final: 0.6472 (mtmm) REVERT: M 36 TYR cc_start: 0.8097 (t80) cc_final: 0.7309 (t80) REVERT: M 60 MET cc_start: 0.7050 (mmm) cc_final: 0.6418 (mtt) REVERT: N 42 LEU cc_start: 0.8861 (mp) cc_final: 0.8647 (mp) REVERT: N 66 MET cc_start: 0.5186 (tpt) cc_final: 0.4572 (tpp) REVERT: O 42 LEU cc_start: 0.7946 (tp) cc_final: 0.7508 (tt) REVERT: O 54 PHE cc_start: 0.7459 (t80) cc_final: 0.6969 (t80) REVERT: P 38 ARG cc_start: 0.4939 (tpm170) cc_final: 0.4522 (tpm170) REVERT: P 62 LEU cc_start: 0.6488 (mm) cc_final: 0.6071 (tp) REVERT: P 66 MET cc_start: 0.7932 (tpt) cc_final: 0.7693 (ttm) REVERT: R 44 GLN cc_start: 0.7737 (mp-120) cc_final: 0.7201 (mm-40) REVERT: R 69 PHE cc_start: 0.6120 (p90) cc_final: 0.5645 (m-10) REVERT: a 46 GLN cc_start: 0.8148 (mt0) cc_final: 0.7884 (mm-40) REVERT: a 66 GLN cc_start: 0.7658 (mp10) cc_final: 0.6970 (mp10) REVERT: a 68 TRP cc_start: 0.7507 (m-10) cc_final: 0.6976 (m-10) REVERT: a 73 MET cc_start: 0.6925 (mmt) cc_final: 0.6588 (mmp) REVERT: a 83 ASN cc_start: 0.7289 (m-40) cc_final: 0.6886 (t0) REVERT: a 101 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.7324 (t0) REVERT: a 104 MET cc_start: 0.5895 (mmp) cc_final: 0.5580 (mtp) REVERT: a 114 ILE cc_start: 0.8041 (mt) cc_final: 0.7801 (mt) REVERT: a 140 MET cc_start: 0.7889 (mpp) cc_final: 0.6860 (tpp) REVERT: a 182 MET cc_start: 0.7744 (tpp) cc_final: 0.7281 (tpp) REVERT: a 225 ASN cc_start: 0.7742 (t0) cc_final: 0.7323 (t0) REVERT: b 7 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7607 (tm-30) REVERT: b 14 PHE cc_start: 0.7045 (m-10) cc_final: 0.6835 (m-80) REVERT: b 19 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8523 (tm-30) REVERT: b 84 LYS cc_start: 0.9159 (tmtt) cc_final: 0.8920 (tttp) REVERT: d 138 VAL cc_start: 0.6580 (t) cc_final: 0.6363 (t) REVERT: d 157 ILE cc_start: 0.7716 (pt) cc_final: 0.7391 (tp) REVERT: e 32 LEU cc_start: 0.5836 (pp) cc_final: 0.5191 (pp) REVERT: e 33 LYS cc_start: 0.7029 (ptpp) cc_final: 0.6204 (mmtt) REVERT: e 46 GLU cc_start: 0.6325 (pp20) cc_final: 0.6087 (pp20) REVERT: g 23 LYS cc_start: 0.4555 (mptt) cc_final: 0.4333 (mmmt) REVERT: j 10 TRP cc_start: 0.8001 (t-100) cc_final: 0.7438 (t60) REVERT: j 14 LYS cc_start: 0.7144 (tmmt) cc_final: 0.6186 (tttt) REVERT: j 39 ARG cc_start: 0.7246 (ttt-90) cc_final: 0.6952 (ttm170) REVERT: k 27 MET cc_start: 0.5240 (ptp) cc_final: 0.3978 (tmm) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.0845 time to fit residues: 45.9436 Evaluate side-chains 277 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 45 GLN a 101 ASN a 168 HIS d 129 GLN j 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.187671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170127 restraints weight = 18383.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.173121 restraints weight = 11009.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175608 restraints weight = 6736.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.176176 restraints weight = 4415.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.176228 restraints weight = 3919.651| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10235 Z= 0.141 Angle : 0.635 8.534 13862 Z= 0.315 Chirality : 0.040 0.176 1622 Planarity : 0.004 0.058 1697 Dihedral : 5.457 57.147 1427 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.20 % Allowed : 5.48 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1257 helix: 1.72 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -0.60 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 40 TYR 0.010 0.001 TYR k 17 PHE 0.028 0.002 PHE R 69 TRP 0.012 0.001 TRP d 152 HIS 0.003 0.001 HIS a 168 Details of bonding type rmsd covalent geometry : bond 0.00312 (10235) covalent geometry : angle 0.63511 (13862) hydrogen bonds : bond 0.04437 ( 761) hydrogen bonds : angle 3.75029 ( 2238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8605 (ppp) cc_final: 0.8270 (tmm) REVERT: 8 13 ILE cc_start: 0.8831 (mm) cc_final: 0.8566 (mm) REVERT: M 7 LYS cc_start: 0.7435 (mttt) cc_final: 0.7214 (mtmm) REVERT: M 36 TYR cc_start: 0.7173 (t80) cc_final: 0.6949 (t80) REVERT: M 60 MET cc_start: 0.8012 (mmm) cc_final: 0.7373 (mtt) REVERT: N 66 MET cc_start: 0.7100 (tpt) cc_final: 0.6287 (tpp) REVERT: O 54 PHE cc_start: 0.8431 (t80) cc_final: 0.8217 (t80) REVERT: P 38 ARG cc_start: 0.5527 (tpm170) cc_final: 0.5013 (tpm170) REVERT: P 44 GLN cc_start: 0.8053 (tp40) cc_final: 0.7814 (tp40) REVERT: Q 58 GLU cc_start: 0.7357 (mp0) cc_final: 0.6953 (mp0) REVERT: R 44 GLN cc_start: 0.7917 (mp-120) cc_final: 0.7630 (mm-40) REVERT: R 69 PHE cc_start: 0.6733 (p90) cc_final: 0.6238 (m-10) REVERT: a 73 MET cc_start: 0.7651 (mmt) cc_final: 0.7124 (mmp) REVERT: a 83 ASN cc_start: 0.8447 (m-40) cc_final: 0.7733 (t0) REVERT: a 104 MET cc_start: 0.7043 (mmp) cc_final: 0.6337 (mtp) REVERT: a 114 ILE cc_start: 0.8724 (mt) cc_final: 0.8461 (mt) REVERT: a 140 MET cc_start: 0.7426 (mpp) cc_final: 0.6880 (tpp) REVERT: a 168 HIS cc_start: 0.7633 (m90) cc_final: 0.7351 (m-70) REVERT: a 182 MET cc_start: 0.8660 (tpp) cc_final: 0.8042 (tpp) REVERT: a 225 ASN cc_start: 0.8132 (t0) cc_final: 0.7758 (t0) REVERT: b 19 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8081 (tm-30) REVERT: d 128 ASP cc_start: 0.7909 (t0) cc_final: 0.7600 (t0) REVERT: e 32 LEU cc_start: 0.5894 (pp) cc_final: 0.5425 (pp) REVERT: e 33 LYS cc_start: 0.7229 (ptpp) cc_final: 0.6112 (mmtt) REVERT: j 10 TRP cc_start: 0.7669 (t-100) cc_final: 0.7284 (t60) REVERT: j 14 LYS cc_start: 0.7847 (tmmt) cc_final: 0.6611 (tttt) REVERT: j 39 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7426 (ttm170) REVERT: k 27 MET cc_start: 0.6241 (ptp) cc_final: 0.5149 (tmm) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 0.0758 time to fit residues: 35.7307 Evaluate side-chains 266 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 69 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 101 ASN j 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.189304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.172413 restraints weight = 18300.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175410 restraints weight = 10082.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177321 restraints weight = 6451.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178459 restraints weight = 4640.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179379 restraints weight = 3714.094| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10235 Z= 0.132 Angle : 0.613 8.436 13862 Z= 0.304 Chirality : 0.040 0.170 1622 Planarity : 0.004 0.052 1697 Dihedral : 5.360 56.581 1427 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.20 % Allowed : 5.00 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.24), residues: 1257 helix: 1.77 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 25 TYR 0.012 0.001 TYR a 221 PHE 0.036 0.002 PHE a 204 TRP 0.010 0.001 TRP g 83 HIS 0.003 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00292 (10235) covalent geometry : angle 0.61317 (13862) hydrogen bonds : bond 0.04201 ( 761) hydrogen bonds : angle 3.65543 ( 2238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8785 (mm) cc_final: 0.8467 (mm) REVERT: 8 27 LYS cc_start: 0.8088 (tptt) cc_final: 0.7386 (ttmm) REVERT: M 36 TYR cc_start: 0.7125 (t80) cc_final: 0.6904 (t80) REVERT: M 60 MET cc_start: 0.8124 (mmm) cc_final: 0.7420 (mtt) REVERT: N 38 ARG cc_start: 0.7829 (mmp-170) cc_final: 0.7364 (ttm170) REVERT: N 66 MET cc_start: 0.7226 (tpt) cc_final: 0.6521 (tpp) REVERT: P 38 ARG cc_start: 0.5504 (tpm170) cc_final: 0.4971 (tpm170) REVERT: P 44 GLN cc_start: 0.8024 (tp40) cc_final: 0.7803 (tp40) REVERT: R 60 MET cc_start: 0.6385 (tpt) cc_final: 0.5665 (tmm) REVERT: R 69 PHE cc_start: 0.6545 (p90) cc_final: 0.6144 (m-10) REVERT: a 83 ASN cc_start: 0.8407 (m-40) cc_final: 0.7692 (t0) REVERT: a 104 MET cc_start: 0.6978 (mmp) cc_final: 0.6410 (ttp) REVERT: a 114 ILE cc_start: 0.8675 (mt) cc_final: 0.8423 (mt) REVERT: a 168 HIS cc_start: 0.7618 (m90) cc_final: 0.7319 (m-70) REVERT: a 182 MET cc_start: 0.8628 (tpp) cc_final: 0.7987 (tpp) REVERT: a 225 ASN cc_start: 0.8147 (t0) cc_final: 0.7669 (t0) REVERT: b 19 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8084 (tm-30) REVERT: b 29 THR cc_start: 0.7341 (m) cc_final: 0.7124 (m) REVERT: e 32 LEU cc_start: 0.5947 (pp) cc_final: 0.5503 (pp) REVERT: e 33 LYS cc_start: 0.7330 (ptpp) cc_final: 0.6281 (mmtt) REVERT: g 81 GLU cc_start: 0.6336 (tp30) cc_final: 0.6092 (tt0) REVERT: j 10 TRP cc_start: 0.7606 (t-100) cc_final: 0.7267 (t60) REVERT: j 14 LYS cc_start: 0.7652 (tmmt) cc_final: 0.6566 (tttt) REVERT: k 27 MET cc_start: 0.6007 (ptp) cc_final: 0.5412 (tmm) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.0763 time to fit residues: 36.3061 Evaluate side-chains 259 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 45 GLN Q 45 GLN a 101 ASN j 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.183046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.166353 restraints weight = 17350.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169195 restraints weight = 9782.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170855 restraints weight = 6445.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172151 restraints weight = 4847.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172898 restraints weight = 3922.900| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10235 Z= 0.135 Angle : 0.622 8.275 13862 Z= 0.310 Chirality : 0.040 0.169 1622 Planarity : 0.004 0.049 1697 Dihedral : 5.352 56.566 1427 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.20 % Allowed : 3.82 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1257 helix: 1.72 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 36 TYR 0.011 0.001 TYR e 24 PHE 0.023 0.002 PHE R 69 TRP 0.010 0.001 TRP g 83 HIS 0.003 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00299 (10235) covalent geometry : angle 0.62214 (13862) hydrogen bonds : bond 0.04165 ( 761) hydrogen bonds : angle 3.69504 ( 2238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 36 TYR cc_start: 0.7151 (t80) cc_final: 0.6924 (t80) REVERT: M 60 MET cc_start: 0.7980 (mmm) cc_final: 0.7422 (mtt) REVERT: N 38 ARG cc_start: 0.7931 (mmp-170) cc_final: 0.7470 (ttm170) REVERT: N 66 MET cc_start: 0.7211 (tpt) cc_final: 0.6509 (tpp) REVERT: O 49 TYR cc_start: 0.7802 (m-80) cc_final: 0.7577 (m-80) REVERT: P 44 GLN cc_start: 0.8029 (tp40) cc_final: 0.7828 (tp40) REVERT: Q 49 TYR cc_start: 0.7834 (m-10) cc_final: 0.7134 (m-80) REVERT: Q 58 GLU cc_start: 0.7420 (mp0) cc_final: 0.7053 (mp0) REVERT: R 60 MET cc_start: 0.6592 (tpt) cc_final: 0.5937 (tmm) REVERT: R 69 PHE cc_start: 0.6592 (p90) cc_final: 0.6180 (m-10) REVERT: a 73 MET cc_start: 0.7577 (mmt) cc_final: 0.6962 (mmp) REVERT: a 83 ASN cc_start: 0.8498 (m-40) cc_final: 0.7874 (t0) REVERT: a 104 MET cc_start: 0.6695 (mmp) cc_final: 0.6449 (ttp) REVERT: a 114 ILE cc_start: 0.8767 (mt) cc_final: 0.8425 (mt) REVERT: a 168 HIS cc_start: 0.7640 (m90) cc_final: 0.7259 (m-70) REVERT: a 182 MET cc_start: 0.8616 (tpp) cc_final: 0.7986 (tpp) REVERT: a 203 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7985 (tm-30) REVERT: a 225 ASN cc_start: 0.8080 (t0) cc_final: 0.7604 (t0) REVERT: b 19 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8007 (tm-30) REVERT: d 138 VAL cc_start: 0.6949 (t) cc_final: 0.6737 (t) REVERT: e 32 LEU cc_start: 0.5994 (pp) cc_final: 0.5510 (pp) REVERT: e 33 LYS cc_start: 0.7309 (ptpp) cc_final: 0.6288 (mmtt) REVERT: j 10 TRP cc_start: 0.7580 (t-100) cc_final: 0.7275 (t60) REVERT: j 14 LYS cc_start: 0.7719 (tmmt) cc_final: 0.6621 (tttt) REVERT: k 27 MET cc_start: 0.5906 (ptp) cc_final: 0.5364 (tmm) outliers start: 2 outliers final: 0 residues processed: 313 average time/residue: 0.0776 time to fit residues: 36.0014 Evaluate side-chains 263 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 ASN j 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166613 restraints weight = 16663.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.169097 restraints weight = 9948.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.170739 restraints weight = 6844.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.171806 restraints weight = 5238.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.172610 restraints weight = 4351.093| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10235 Z= 0.148 Angle : 0.639 8.199 13862 Z= 0.321 Chirality : 0.041 0.163 1622 Planarity : 0.004 0.049 1697 Dihedral : 5.393 55.183 1427 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1257 helix: 1.63 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 122 TYR 0.016 0.001 TYR a 221 PHE 0.040 0.002 PHE a 204 TRP 0.011 0.001 TRP g 83 HIS 0.003 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00336 (10235) covalent geometry : angle 0.63871 (13862) hydrogen bonds : bond 0.04371 ( 761) hydrogen bonds : angle 3.77609 ( 2238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 39 LEU cc_start: 0.7186 (pt) cc_final: 0.6985 (pp) REVERT: M 3 ASP cc_start: 0.7389 (p0) cc_final: 0.6988 (p0) REVERT: M 7 LYS cc_start: 0.7804 (mppt) cc_final: 0.7225 (mppt) REVERT: M 32 LEU cc_start: 0.9148 (tt) cc_final: 0.8921 (tt) REVERT: M 36 TYR cc_start: 0.7085 (t80) cc_final: 0.6881 (t80) REVERT: M 60 MET cc_start: 0.8065 (mmm) cc_final: 0.7480 (mtt) REVERT: N 38 ARG cc_start: 0.7961 (mmp-170) cc_final: 0.7510 (ttm170) REVERT: N 66 MET cc_start: 0.7241 (tpt) cc_final: 0.6493 (tpp) REVERT: O 54 PHE cc_start: 0.8452 (t80) cc_final: 0.8155 (t80) REVERT: P 44 GLN cc_start: 0.8041 (tp40) cc_final: 0.7776 (tp40) REVERT: R 56 LEU cc_start: 0.8288 (tp) cc_final: 0.8081 (tp) REVERT: R 60 MET cc_start: 0.6534 (tpt) cc_final: 0.5931 (tmm) REVERT: R 69 PHE cc_start: 0.6557 (p90) cc_final: 0.6221 (m-10) REVERT: a 83 ASN cc_start: 0.8635 (m-40) cc_final: 0.7815 (t0) REVERT: a 104 MET cc_start: 0.6936 (mmp) cc_final: 0.6599 (ttm) REVERT: a 114 ILE cc_start: 0.8674 (mt) cc_final: 0.8306 (mt) REVERT: a 182 MET cc_start: 0.8548 (tpp) cc_final: 0.7909 (tpp) REVERT: a 225 ASN cc_start: 0.8151 (t0) cc_final: 0.7755 (t0) REVERT: b 19 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7922 (tm-30) REVERT: e 32 LEU cc_start: 0.5865 (pp) cc_final: 0.5487 (pp) REVERT: e 33 LYS cc_start: 0.6799 (pttm) cc_final: 0.6079 (mmtt) REVERT: j 10 TRP cc_start: 0.7580 (t-100) cc_final: 0.7270 (t60) REVERT: j 14 LYS cc_start: 0.7779 (tmmt) cc_final: 0.6799 (tttt) REVERT: k 27 MET cc_start: 0.6111 (ptp) cc_final: 0.5556 (tmm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.0785 time to fit residues: 36.0738 Evaluate side-chains 256 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 0.0010 chunk 95 optimal weight: 0.0670 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 45 GLN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** f 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.172104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153408 restraints weight = 17686.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156489 restraints weight = 10187.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159288 restraints weight = 6689.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.159928 restraints weight = 4303.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.160019 restraints weight = 3782.363| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10235 Z= 0.130 Angle : 0.627 7.877 13862 Z= 0.311 Chirality : 0.040 0.183 1622 Planarity : 0.004 0.049 1697 Dihedral : 5.380 57.380 1427 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1257 helix: 1.67 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 122 TYR 0.023 0.001 TYR M 49 PHE 0.023 0.001 PHE f 37 TRP 0.009 0.001 TRP g 83 HIS 0.003 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00280 (10235) covalent geometry : angle 0.62725 (13862) hydrogen bonds : bond 0.04115 ( 761) hydrogen bonds : angle 3.71085 ( 2238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 32 LEU cc_start: 0.9195 (tt) cc_final: 0.8953 (tt) REVERT: M 36 TYR cc_start: 0.7210 (t80) cc_final: 0.6901 (t80) REVERT: M 44 GLN cc_start: 0.8337 (pp30) cc_final: 0.8070 (pp30) REVERT: M 60 MET cc_start: 0.7968 (mmm) cc_final: 0.7378 (mtt) REVERT: N 38 ARG cc_start: 0.8073 (mmp-170) cc_final: 0.7538 (ttm170) REVERT: N 66 MET cc_start: 0.6988 (tpt) cc_final: 0.6171 (tpp) REVERT: O 52 LEU cc_start: 0.7859 (tt) cc_final: 0.7125 (mm) REVERT: P 38 ARG cc_start: 0.4905 (tpm170) cc_final: 0.4643 (tpt170) REVERT: P 44 GLN cc_start: 0.8037 (tp40) cc_final: 0.7767 (tp40) REVERT: Q 58 GLU cc_start: 0.7434 (mp0) cc_final: 0.6831 (mp0) REVERT: R 56 LEU cc_start: 0.8273 (tp) cc_final: 0.8032 (tp) REVERT: R 60 MET cc_start: 0.6466 (tpt) cc_final: 0.5842 (tmm) REVERT: R 69 PHE cc_start: 0.6514 (p90) cc_final: 0.6046 (m-10) REVERT: a 73 MET cc_start: 0.7369 (mmt) cc_final: 0.6800 (mmp) REVERT: a 104 MET cc_start: 0.6996 (mmp) cc_final: 0.6451 (ttm) REVERT: a 114 ILE cc_start: 0.8698 (mt) cc_final: 0.8335 (mt) REVERT: a 225 ASN cc_start: 0.8089 (t0) cc_final: 0.7658 (t0) REVERT: b 19 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8205 (tm-30) REVERT: b 81 PHE cc_start: 0.8413 (t80) cc_final: 0.8090 (t80) REVERT: d 138 VAL cc_start: 0.6886 (t) cc_final: 0.6679 (t) REVERT: e 32 LEU cc_start: 0.5903 (pp) cc_final: 0.5355 (pp) REVERT: e 33 LYS cc_start: 0.6782 (pttm) cc_final: 0.5943 (mmtt) REVERT: j 10 TRP cc_start: 0.7776 (t-100) cc_final: 0.7296 (t60) REVERT: j 14 LYS cc_start: 0.7875 (tmmt) cc_final: 0.6676 (tttt) REVERT: k 27 MET cc_start: 0.6609 (ptp) cc_final: 0.5724 (tmm) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.0756 time to fit residues: 35.3188 Evaluate side-chains 267 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 101 ASN a 168 HIS f 70 ASN j 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151511 restraints weight = 17318.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154525 restraints weight = 10297.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157390 restraints weight = 6786.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.157648 restraints weight = 4552.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157800 restraints weight = 4066.910| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10235 Z= 0.153 Angle : 0.653 7.996 13862 Z= 0.330 Chirality : 0.041 0.162 1622 Planarity : 0.004 0.050 1697 Dihedral : 5.417 55.915 1427 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1257 helix: 1.60 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 40 TYR 0.019 0.001 TYR a 221 PHE 0.025 0.002 PHE f 37 TRP 0.013 0.001 TRP g 83 HIS 0.005 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00348 (10235) covalent geometry : angle 0.65278 (13862) hydrogen bonds : bond 0.04330 ( 761) hydrogen bonds : angle 3.88426 ( 2238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 ASP cc_start: 0.7038 (p0) cc_final: 0.6601 (p0) REVERT: M 7 LYS cc_start: 0.7337 (mppt) cc_final: 0.6927 (mppt) REVERT: M 36 TYR cc_start: 0.7273 (t80) cc_final: 0.6927 (t80) REVERT: M 44 GLN cc_start: 0.8308 (pp30) cc_final: 0.7923 (pp30) REVERT: N 38 ARG cc_start: 0.8088 (mmp-170) cc_final: 0.7488 (ttm170) REVERT: N 66 MET cc_start: 0.7125 (tpt) cc_final: 0.6342 (tpp) REVERT: P 38 ARG cc_start: 0.3877 (tpm170) cc_final: 0.3594 (tpt170) REVERT: Q 49 TYR cc_start: 0.7669 (m-10) cc_final: 0.6889 (m-80) REVERT: Q 58 GLU cc_start: 0.7596 (mp0) cc_final: 0.7145 (mp0) REVERT: R 56 LEU cc_start: 0.8267 (tp) cc_final: 0.7941 (tp) REVERT: R 60 MET cc_start: 0.6514 (tpt) cc_final: 0.5887 (tmm) REVERT: R 69 PHE cc_start: 0.6758 (p90) cc_final: 0.6096 (m-10) REVERT: a 73 MET cc_start: 0.7678 (mmt) cc_final: 0.7098 (mmp) REVERT: a 104 MET cc_start: 0.6676 (mmp) cc_final: 0.6407 (ttm) REVERT: a 114 ILE cc_start: 0.8607 (mt) cc_final: 0.8205 (mt) REVERT: a 225 ASN cc_start: 0.7964 (t0) cc_final: 0.7587 (t0) REVERT: b 19 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8157 (tm-30) REVERT: e 32 LEU cc_start: 0.5987 (pp) cc_final: 0.5437 (pp) REVERT: e 33 LYS cc_start: 0.7012 (pttm) cc_final: 0.6158 (mmtt) REVERT: j 10 TRP cc_start: 0.7568 (t-100) cc_final: 0.7145 (t60) REVERT: j 14 LYS cc_start: 0.7981 (tmmt) cc_final: 0.6743 (tttt) REVERT: k 27 MET cc_start: 0.6695 (ptp) cc_final: 0.5804 (tmm) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.0821 time to fit residues: 36.9335 Evaluate side-chains 256 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 111 optimal weight: 0.0470 chunk 26 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 93 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 45 GLN a 101 ASN a 168 HIS d 129 GLN f 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155744 restraints weight = 17271.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159046 restraints weight = 9901.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162181 restraints weight = 6229.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162603 restraints weight = 3936.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.162754 restraints weight = 3515.804| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10235 Z= 0.133 Angle : 0.638 7.886 13862 Z= 0.316 Chirality : 0.040 0.193 1622 Planarity : 0.004 0.049 1697 Dihedral : 5.366 57.968 1427 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.24), residues: 1257 helix: 1.65 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 38 TYR 0.019 0.001 TYR M 49 PHE 0.029 0.002 PHE K 63 TRP 0.009 0.001 TRP g 83 HIS 0.004 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00287 (10235) covalent geometry : angle 0.63799 (13862) hydrogen bonds : bond 0.04050 ( 761) hydrogen bonds : angle 3.73083 ( 2238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 ASP cc_start: 0.6769 (p0) cc_final: 0.6329 (p0) REVERT: M 7 LYS cc_start: 0.7400 (mppt) cc_final: 0.7031 (mppt) REVERT: M 36 TYR cc_start: 0.7310 (t80) cc_final: 0.6931 (t80) REVERT: M 44 GLN cc_start: 0.8430 (pp30) cc_final: 0.8043 (pp30) REVERT: M 60 MET cc_start: 0.7762 (mmm) cc_final: 0.7287 (mtt) REVERT: N 38 ARG cc_start: 0.8035 (mmp-170) cc_final: 0.7427 (ttm170) REVERT: N 66 MET cc_start: 0.7037 (tpt) cc_final: 0.6329 (tpp) REVERT: O 52 LEU cc_start: 0.7993 (tt) cc_final: 0.7265 (mm) REVERT: P 38 ARG cc_start: 0.4827 (tpm170) cc_final: 0.4577 (tpt170) REVERT: P 44 GLN cc_start: 0.7988 (tp40) cc_final: 0.7644 (tp40) REVERT: R 56 LEU cc_start: 0.8075 (tp) cc_final: 0.7762 (tp) REVERT: R 60 MET cc_start: 0.6452 (tpt) cc_final: 0.5846 (tmm) REVERT: R 66 MET cc_start: 0.7847 (tmm) cc_final: 0.7459 (tmm) REVERT: R 69 PHE cc_start: 0.6711 (p90) cc_final: 0.6139 (m-10) REVERT: a 114 ILE cc_start: 0.8550 (mt) cc_final: 0.8129 (mt) REVERT: a 225 ASN cc_start: 0.8016 (t0) cc_final: 0.7609 (t0) REVERT: b 19 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8230 (tm-30) REVERT: b 81 PHE cc_start: 0.8372 (t80) cc_final: 0.8053 (t80) REVERT: b 87 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7353 (pt0) REVERT: e 32 LEU cc_start: 0.5876 (pp) cc_final: 0.5345 (pp) REVERT: e 33 LYS cc_start: 0.6957 (pttm) cc_final: 0.6115 (mmtt) REVERT: j 10 TRP cc_start: 0.7644 (t-100) cc_final: 0.7226 (t60) REVERT: j 14 LYS cc_start: 0.7840 (tmmt) cc_final: 0.6621 (tttm) REVERT: k 27 MET cc_start: 0.6550 (ptp) cc_final: 0.5672 (tmm) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.0813 time to fit residues: 38.3900 Evaluate side-chains 263 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 36 ASN Q 45 GLN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 119 ASN a 168 HIS f 70 ASN j 22 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.174709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156772 restraints weight = 17271.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159334 restraints weight = 10330.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162242 restraints weight = 7426.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.162726 restraints weight = 4577.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163113 restraints weight = 4178.252| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10235 Z= 0.142 Angle : 0.668 9.674 13862 Z= 0.329 Chirality : 0.040 0.174 1622 Planarity : 0.004 0.049 1697 Dihedral : 5.426 57.566 1427 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.10 % Allowed : 0.69 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1257 helix: 1.62 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 122 TYR 0.022 0.001 TYR a 221 PHE 0.037 0.002 PHE Q 73 TRP 0.010 0.001 TRP g 83 HIS 0.003 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00319 (10235) covalent geometry : angle 0.66779 (13862) hydrogen bonds : bond 0.04132 ( 761) hydrogen bonds : angle 3.81860 ( 2238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 ASP cc_start: 0.6796 (p0) cc_final: 0.6289 (p0) REVERT: M 7 LYS cc_start: 0.7553 (mppt) cc_final: 0.7108 (mppt) REVERT: M 36 TYR cc_start: 0.7233 (t80) cc_final: 0.6905 (t80) REVERT: M 44 GLN cc_start: 0.8289 (pp30) cc_final: 0.7863 (pp30) REVERT: M 60 MET cc_start: 0.7812 (mmm) cc_final: 0.7324 (mtt) REVERT: N 38 ARG cc_start: 0.7968 (mmp-170) cc_final: 0.7456 (ttm170) REVERT: N 66 MET cc_start: 0.7105 (tpt) cc_final: 0.6413 (tpp) REVERT: O 52 LEU cc_start: 0.8086 (tt) cc_final: 0.7248 (mm) REVERT: P 38 ARG cc_start: 0.4197 (tpm170) cc_final: 0.3840 (tpt170) REVERT: Q 49 TYR cc_start: 0.7687 (m-10) cc_final: 0.6894 (m-80) REVERT: R 56 LEU cc_start: 0.8156 (tp) cc_final: 0.7837 (tp) REVERT: R 60 MET cc_start: 0.6511 (tpt) cc_final: 0.5931 (tmm) REVERT: R 66 MET cc_start: 0.7932 (tmm) cc_final: 0.7534 (tmm) REVERT: R 69 PHE cc_start: 0.6704 (p90) cc_final: 0.6278 (m-10) REVERT: a 114 ILE cc_start: 0.8588 (mt) cc_final: 0.8201 (mt) REVERT: a 140 MET cc_start: 0.7506 (mpp) cc_final: 0.6938 (tpp) REVERT: a 225 ASN cc_start: 0.7856 (t0) cc_final: 0.7461 (t0) REVERT: b 19 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8161 (tm-30) REVERT: b 81 PHE cc_start: 0.8417 (t80) cc_final: 0.8120 (t80) REVERT: e 32 LEU cc_start: 0.6058 (pp) cc_final: 0.5543 (pp) REVERT: e 33 LYS cc_start: 0.6914 (pttm) cc_final: 0.6111 (mmtt) REVERT: j 10 TRP cc_start: 0.7576 (t-100) cc_final: 0.7104 (t60) REVERT: j 14 LYS cc_start: 0.7735 (tmmt) cc_final: 0.6581 (tttm) REVERT: k 27 MET cc_start: 0.6524 (ptp) cc_final: 0.5638 (tmm) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.0774 time to fit residues: 35.9370 Evaluate side-chains 264 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 86 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 55 optimal weight: 0.2980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 45 GLN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS f 70 ASN j 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.156765 restraints weight = 17232.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159076 restraints weight = 10117.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.161987 restraints weight = 7062.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.162015 restraints weight = 4683.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162233 restraints weight = 4314.313| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10235 Z= 0.134 Angle : 0.655 9.539 13862 Z= 0.323 Chirality : 0.040 0.210 1622 Planarity : 0.004 0.051 1697 Dihedral : 5.342 57.841 1427 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1257 helix: 1.61 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 122 TYR 0.017 0.001 TYR k 34 PHE 0.031 0.002 PHE Q 73 TRP 0.008 0.001 TRP g 83 HIS 0.004 0.000 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00293 (10235) covalent geometry : angle 0.65526 (13862) hydrogen bonds : bond 0.03959 ( 761) hydrogen bonds : angle 3.78519 ( 2238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 3 ASP cc_start: 0.6948 (p0) cc_final: 0.6464 (p0) REVERT: M 7 LYS cc_start: 0.7467 (mppt) cc_final: 0.7033 (mppt) REVERT: M 36 TYR cc_start: 0.7268 (t80) cc_final: 0.6879 (t80) REVERT: M 44 GLN cc_start: 0.8251 (pp30) cc_final: 0.7885 (pp30) REVERT: M 60 MET cc_start: 0.7692 (mmm) cc_final: 0.7412 (mtt) REVERT: N 38 ARG cc_start: 0.7980 (mmp-170) cc_final: 0.7327 (ttm170) REVERT: N 66 MET cc_start: 0.6962 (tpt) cc_final: 0.6307 (tpp) REVERT: O 52 LEU cc_start: 0.7866 (tt) cc_final: 0.7138 (mm) REVERT: P 38 ARG cc_start: 0.4162 (tpm170) cc_final: 0.3602 (tpt170) REVERT: P 46 LEU cc_start: 0.7865 (mt) cc_final: 0.7555 (mt) REVERT: R 56 LEU cc_start: 0.8071 (tp) cc_final: 0.7763 (tp) REVERT: R 60 MET cc_start: 0.6289 (tpt) cc_final: 0.5708 (tmm) REVERT: R 66 MET cc_start: 0.7872 (tmm) cc_final: 0.7498 (tmm) REVERT: R 69 PHE cc_start: 0.7008 (p90) cc_final: 0.6351 (m-10) REVERT: a 104 MET cc_start: 0.7992 (ttm) cc_final: 0.7710 (ttm) REVERT: a 114 ILE cc_start: 0.8554 (mt) cc_final: 0.8140 (mt) REVERT: a 140 MET cc_start: 0.7609 (mpp) cc_final: 0.6921 (tpp) REVERT: a 225 ASN cc_start: 0.8086 (t0) cc_final: 0.7603 (t0) REVERT: b 19 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8265 (tm-30) REVERT: b 81 PHE cc_start: 0.8310 (t80) cc_final: 0.8026 (t80) REVERT: e 32 LEU cc_start: 0.5881 (pp) cc_final: 0.5357 (pp) REVERT: e 33 LYS cc_start: 0.6931 (pttm) cc_final: 0.6102 (mmtt) REVERT: f 66 TYR cc_start: 0.7538 (t80) cc_final: 0.7093 (t80) REVERT: j 10 TRP cc_start: 0.7715 (t-100) cc_final: 0.7229 (t60) REVERT: j 14 LYS cc_start: 0.7671 (tmmt) cc_final: 0.6482 (tttm) REVERT: k 27 MET cc_start: 0.6467 (ptp) cc_final: 0.5560 (tmm) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.0807 time to fit residues: 36.6188 Evaluate side-chains 261 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS f 70 ASN j 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.152478 restraints weight = 17497.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.155672 restraints weight = 10109.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158455 restraints weight = 6412.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159099 restraints weight = 4240.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159175 restraints weight = 3734.291| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10235 Z= 0.146 Angle : 0.685 9.765 13862 Z= 0.341 Chirality : 0.042 0.216 1622 Planarity : 0.004 0.049 1697 Dihedral : 5.404 56.224 1427 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1257 helix: 1.59 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 122 TYR 0.037 0.001 TYR O 36 PHE 0.029 0.002 PHE Q 73 TRP 0.013 0.001 TRP g 83 HIS 0.003 0.001 HIS d 154 Details of bonding type rmsd covalent geometry : bond 0.00332 (10235) covalent geometry : angle 0.68548 (13862) hydrogen bonds : bond 0.04281 ( 761) hydrogen bonds : angle 3.83127 ( 2238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.52 seconds wall clock time: 30 minutes 36.86 seconds (1836.86 seconds total)