Starting phenix.real_space_refine on Mon Nov 17 22:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cp7_7549/11_2025/6cp7_7549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp7_7549/11_2025/6cp7_7549.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 { model { file = "/net/cci-nas-00/data/ceres_data/6cp7_7549/11_2025/6cp7_7549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp7_7549/11_2025/6cp7_7549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cp7_7549/11_2025/6cp7_7549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp7_7549/11_2025/6cp7_7549.map" } 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 ------------------------------------------------------------------------------- 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= 0.006 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 51 5.16 5 C 6129 2.51 5 N 1423 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9164 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 534 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 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} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 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} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 522 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1760 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 393 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 520 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 63} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 522 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 63} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 2.23, per 1000 atoms: 0.24 Number of scatterers: 9164 At special positions: 0 Unit cell: (84.87, 113.16, 114.39, 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 51 16.00 O 1561 8.00 N 1423 7.00 C 6129 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: 0.95 Conformation dependent library (CDL) restraints added in 334.0 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 19 through 38 removed outlier: 3.875A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 43 through 57 Proline residue: K 49 - end of helix removed outlier: 3.658A pdb=" N ALA K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 63 No H-bonds generated for 'chain 'K' and resid 61 through 63' Processing helix chain 'K' and resid 64 through 74 Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 18 through 38 removed outlier: 3.866A pdb=" N ALA L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 43 through 72 Proline residue: L 49 - end of helix removed outlier: 4.338A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 removed outlier: 4.327A pdb=" N ALA M 6 " --> pdb=" O GLN M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 18 No H-bonds generated for 'chain 'M' and resid 16 through 18' Processing helix chain 'M' and resid 19 through 38 removed outlier: 4.552A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 42 No H-bonds generated for 'chain 'M' and resid 40 through 42' Processing helix chain 'M' and resid 43 through 57 Proline residue: M 49 - end of helix removed outlier: 3.694A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 74 removed outlier: 3.532A pdb=" N VAL M 68 " --> pdb=" O PHE M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 18 through 38 removed outlier: 4.202A pdb=" N ALA N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA N 27 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER N 38 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 removed outlier: 3.715A pdb=" N VAL N 47 " --> pdb=" O ILE N 43 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 4.688A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 15 through 18 removed outlier: 4.108A pdb=" N GLY O 18 " --> pdb=" O SER O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 15 through 18' Processing helix chain 'O' and resid 19 through 24 Processing helix chain 'O' and resid 25 through 38 removed outlier: 3.637A pdb=" N PHE O 30 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 42 No H-bonds generated for 'chain 'O' and resid 40 through 42' Processing helix chain 'O' and resid 43 through 74 Proline residue: O 49 - end of helix removed outlier: 3.753A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 removed outlier: 4.071A pdb=" N ALA P 6 " --> pdb=" O GLN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 38 removed outlier: 4.919A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 74 removed outlier: 3.807A pdb=" N MET P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 removed outlier: 3.794A pdb=" N ALA Q 6 " --> pdb=" O GLN Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 18 No H-bonds generated for 'chain 'Q' and resid 16 through 18' Processing helix chain 'Q' and resid 19 through 24 removed outlier: 3.823A pdb=" N ILE Q 24 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 38 Processing helix chain 'Q' and resid 47 through 74 removed outlier: 4.125A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 Processing helix chain 'R' and resid 19 through 40 removed outlier: 3.860A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 57 Proline residue: R 49 - end of helix Processing helix chain 'R' and resid 58 through 75 removed outlier: 3.877A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS R 65 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU R 73 " --> pdb=" O SER R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 removed outlier: 4.301A pdb=" N ALA S 6 " --> pdb=" O GLN S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 19 through 39 removed outlier: 4.301A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE S 28 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG S 39 " --> pdb=" O ASN S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.555A pdb=" N ILE S 43 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 40 through 44' Processing helix chain 'S' and resid 47 through 74 removed outlier: 3.853A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS S 65 " --> pdb=" O THR S 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 16 through 18 No H-bonds generated for 'chain 'T' and resid 16 through 18' Processing helix chain 'T' and resid 19 through 38 removed outlier: 4.544A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 62 Proline residue: T 49 - end of helix removed outlier: 3.740A pdb=" N LEU T 53 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR T 61 " --> pdb=" O LEU T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 72 Processing helix chain '8' and resid 8 through 31 removed outlier: 3.732A pdb=" N GLN 8 12 " --> pdb=" O TYR 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 32 through 47 removed outlier: 3.879A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 42 Processing helix chain 'X' and resid 56 through 77 removed outlier: 3.918A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE X 77 " --> pdb=" O THR X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 84 No H-bonds generated for 'chain 'X' and resid 82 through 84' Processing helix chain 'X' and resid 85 through 103 removed outlier: 3.829A pdb=" N PHE X 93 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU X 101 " --> pdb=" O PHE X 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER X 103 " --> pdb=" O ALA X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 138 Processing helix chain 'X' and resid 139 through 146 removed outlier: 3.971A pdb=" N PHE X 142 " --> pdb=" O TRP X 139 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL X 146 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 153 No H-bonds generated for 'chain 'X' and resid 151 through 153' Processing helix chain 'X' and resid 154 through 162 removed outlier: 4.263A pdb=" N LEU X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL X 159 " --> pdb=" O VAL X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 198 removed outlier: 4.285A pdb=" N ALA X 170 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE X 171 " --> pdb=" O PHE X 167 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 207 removed outlier: 3.757A pdb=" N LEU X 206 " --> pdb=" O LEU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 247 removed outlier: 3.592A pdb=" N ALA X 225 " --> pdb=" O MET X 221 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR X 247 " --> pdb=" O LYS X 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 104 removed outlier: 3.808A pdb=" N LEU Z 58 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.955A pdb=" N LYS Z 104 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 125 removed outlier: 3.839A pdb=" N GLU 7 113 " --> pdb=" O LEU 7 109 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU 7 117 " --> pdb=" O GLU 7 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN 7 118 " --> pdb=" O LEU 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 142 through 156 removed outlier: 4.509A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 30 Processing helix chain 'U' and resid 48 through 56 Processing helix chain 'U' and resid 63 through 85 removed outlier: 3.609A pdb=" N TRP U 67 " --> pdb=" O GLY U 63 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 34 686 hydrogen bonds defined for protein. 2043 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: 1.30 Time building geometry restraints manager: 1.12 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: 2542 1.34 - 1.46: 1979 1.46 - 1.58: 4728 1.58 - 1.70: 0 1.70 - 1.81: 92 Bond restraints: 9341 Sorted by residual: bond pdb=" C PHE R 48 " pdb=" N PRO R 49 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C LEU X 152 " pdb=" N PRO X 153 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.01e+00 bond pdb=" C PHE M 48 " pdb=" N PRO M 49 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.30e-02 5.92e+03 7.18e+00 bond pdb=" SD FME K 1 " pdb=" CE FME K 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" SD FME P 1 " pdb=" CE FME P 1 " ideal model delta sigma weight residual 1.805 1.754 0.051 2.00e-02 2.50e+03 6.48e+00 ... (remaining 9336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 12090 3.03 - 6.06: 459 6.06 - 9.08: 79 9.08 - 12.11: 20 12.11 - 15.14: 6 Bond angle restraints: 12654 Sorted by residual: angle pdb=" N GLU O 59 " pdb=" CA GLU O 59 " pdb=" C GLU O 59 " ideal model delta sigma weight residual 112.23 105.24 6.99 1.26e+00 6.30e-01 3.08e+01 angle pdb=" O VAL X 155 " pdb=" C VAL X 155 " pdb=" N PRO X 156 " ideal model delta sigma weight residual 120.42 123.94 -3.52 6.40e-01 2.44e+00 3.03e+01 angle pdb=" N GLY S 25 " pdb=" CA GLY S 25 " pdb=" C GLY S 25 " ideal model delta sigma weight residual 112.49 118.90 -6.41 1.21e+00 6.83e-01 2.80e+01 angle pdb=" N GLY T 25 " pdb=" CA GLY T 25 " pdb=" C GLY T 25 " ideal model delta sigma weight residual 112.49 118.72 -6.23 1.21e+00 6.83e-01 2.65e+01 angle pdb=" C ASN X 49 " pdb=" N ASN X 50 " pdb=" CA ASN X 50 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 ... (remaining 12649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4972 17.62 - 35.23: 344 35.23 - 52.85: 63 52.85 - 70.46: 11 70.46 - 88.08: 4 Dihedral angle restraints: 5394 sinusoidal: 1915 harmonic: 3479 Sorted by residual: dihedral pdb=" CA ALA U 75 " pdb=" C ALA U 75 " pdb=" N PHE U 76 " pdb=" CA PHE U 76 " ideal model delta harmonic sigma weight residual 180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA LEU R 19 " pdb=" C LEU R 19 " pdb=" N LEU R 20 " pdb=" CA LEU R 20 " ideal model delta harmonic sigma weight residual 180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA LEU M 19 " pdb=" C LEU M 19 " pdb=" N LEU M 20 " pdb=" CA LEU M 20 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 5391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1366 0.098 - 0.196: 172 0.196 - 0.293: 15 0.293 - 0.391: 3 0.391 - 0.489: 2 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CB ILE O 14 " pdb=" CA ILE O 14 " pdb=" CG1 ILE O 14 " pdb=" CG2 ILE O 14 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CB ILE P 14 " pdb=" CA ILE P 14 " pdb=" CG1 ILE P 14 " pdb=" CG2 ILE P 14 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE K 28 " pdb=" CA ILE K 28 " pdb=" CG1 ILE K 28 " pdb=" CG2 ILE K 28 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1555 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 40 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO L 41 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO L 41 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 41 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 31 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ALA M 31 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA M 31 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA M 32 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE N 28 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C ILE N 28 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE N 28 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL N 29 " 0.017 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 47 2.48 - 3.09: 6540 3.09 - 3.69: 15187 3.69 - 4.30: 21134 4.30 - 4.90: 32958 Nonbonded interactions: 75866 Sorted by model distance: nonbonded pdb=" O LEU X 164 " pdb=" CB ALA X 168 " model vdw 1.876 2.768 nonbonded pdb=" O ILE Q 24 " pdb=" N ILE Q 26 " model vdw 1.947 3.120 nonbonded pdb=" O SER M 58 " pdb=" N ALA M 60 " model vdw 2.043 3.120 nonbonded pdb=" O ILE L 28 " pdb=" N ALA L 31 " model vdw 2.060 3.120 nonbonded pdb=" O GLY Q 54 " pdb=" CB SER Q 58 " model vdw 2.084 2.752 ... (remaining 75861 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' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 56 or (resid 57 through 58 and (name N or name CA or name C or name O or name CB \ )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or name \ O or name CB )) or resid 62 through 74)) selection = (chain 'L' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 56 or (resid 57 throug \ h 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or re \ sid 62 through 74)) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 74)) selection = (chain 'N' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 through 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 through 74)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or n \ ame C or name O or name CB )) or resid 62 through 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 57 or (resi \ d 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or re \ sid 62 through 74)) selection = (chain 'Q' and (resid 1 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 74)) selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 57 or (resid 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 through 74)) selection = (chain 'S' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 through 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 through 74)) selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 through 58 and (name N or name CA or name C or name \ O or name CB )) or resid 59 through 60 or (resid 61 and (name N or name CA or n \ ame C or name O or name CB )) or resid 62 through 74)) } 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: 2.130 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.150 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.008 0.099 9341 Z= 0.377 Angle : 1.418 15.141 12654 Z= 0.741 Chirality : 0.068 0.489 1558 Planarity : 0.009 0.087 1537 Dihedral : 13.158 88.077 3168 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.63 % Favored : 92.87 % Rotamer: Outliers : 3.98 % Allowed : 11.41 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.99 (0.18), residues: 1192 helix: -3.07 (0.12), residues: 947 sheet: None (None), residues: 0 loop : -3.16 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 176 TYR 0.026 0.003 TYR U 51 PHE 0.034 0.004 PHE X 224 TRP 0.031 0.004 TRP X 234 HIS 0.012 0.003 HIS X 114 Details of bonding type rmsd covalent geometry : bond 0.00837 ( 9341) covalent geometry : angle 1.41839 (12654) hydrogen bonds : bond 0.18911 ( 686) hydrogen bonds : angle 8.03685 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 517 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 14 ILE cc_start: 0.7397 (pt) cc_final: 0.7035 (mt) REVERT: L 39 ARG cc_start: 0.7465 (ptm-80) cc_final: 0.6991 (tmt-80) REVERT: M 28 ILE cc_start: 0.9312 (pt) cc_final: 0.8969 (tt) REVERT: M 39 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6961 (tpm170) REVERT: M 59 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: M 67 MET cc_start: 0.7624 (pp-130) cc_final: 0.6720 (pp-130) REVERT: R 47 VAL cc_start: 0.8822 (m) cc_final: 0.8402 (t) REVERT: R 65 CYS cc_start: 0.7002 (t) cc_final: 0.6800 (t) REVERT: S 2 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7691 (pm20) REVERT: S 10 ILE cc_start: 0.8541 (pp) cc_final: 0.8258 (tt) REVERT: S 14 ILE cc_start: 0.9153 (pt) cc_final: 0.8516 (mt) REVERT: S 28 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8021 (pt) REVERT: S 39 ARG cc_start: 0.6827 (ppp80) cc_final: 0.5901 (tpt170) REVERT: S 66 LEU cc_start: 0.8009 (pt) cc_final: 0.7802 (pt) REVERT: T 67 MET cc_start: 0.8193 (pp-130) cc_final: 0.7373 (tmm) REVERT: X 46 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5016 (mm) REVERT: X 53 ILE cc_start: 0.5247 (mt) cc_final: 0.5029 (mp) REVERT: X 169 ARG cc_start: 0.7113 (ttm170) cc_final: 0.6541 (ptm160) REVERT: X 180 ASN cc_start: 0.5601 (m-40) cc_final: 0.5378 (m-40) REVERT: X 194 LEU cc_start: 0.7989 (tt) cc_final: 0.7435 (tt) outliers start: 37 outliers final: 15 residues processed: 533 average time/residue: 0.0831 time to fit residues: 63.8389 Evaluate side-chains 402 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 383 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.0040 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN P 35 ASN Z 93 ASN U 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.111461 restraints weight = 25415.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113506 restraints weight = 16988.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115791 restraints weight = 11257.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.115914 restraints weight = 8162.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.115995 restraints weight = 7886.939| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9341 Z= 0.172 Angle : 0.876 10.849 12654 Z= 0.418 Chirality : 0.046 0.290 1558 Planarity : 0.006 0.058 1537 Dihedral : 6.524 56.412 1276 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.32 % Allowed : 6.14 % Favored : 93.54 % 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: -2.98 (0.21), residues: 1192 helix: -1.60 (0.14), residues: 985 sheet: None (None), residues: 0 loop : -2.82 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 50 TYR 0.032 0.002 TYR X 241 PHE 0.031 0.002 PHE X 167 TRP 0.019 0.002 TRP X 234 HIS 0.007 0.002 HIS X 185 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9341) covalent geometry : angle 0.87621 (12654) hydrogen bonds : bond 0.05002 ( 686) hydrogen bonds : angle 5.35202 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 478 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7792 (mp) cc_final: 0.7335 (tp) REVERT: K 64 PHE cc_start: 0.7617 (m-10) cc_final: 0.7220 (m-10) REVERT: L 20 LEU cc_start: 0.8177 (tp) cc_final: 0.7917 (tp) REVERT: L 39 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.6671 (tmt-80) REVERT: M 4 VAL cc_start: 0.7153 (p) cc_final: 0.6948 (m) REVERT: M 39 ARG cc_start: 0.7371 (mtt-85) cc_final: 0.6931 (tpm170) REVERT: N 53 LEU cc_start: 0.8187 (tt) cc_final: 0.7674 (mt) REVERT: O 15 SER cc_start: 0.7160 (p) cc_final: 0.6959 (p) REVERT: O 35 ASN cc_start: 0.8436 (t0) cc_final: 0.8049 (t0) REVERT: O 64 PHE cc_start: 0.7547 (m-10) cc_final: 0.7324 (m-10) REVERT: O 66 LEU cc_start: 0.8485 (pt) cc_final: 0.8273 (tt) REVERT: P 24 ILE cc_start: 0.9413 (mt) cc_final: 0.9202 (mt) REVERT: P 58 SER cc_start: 0.9146 (t) cc_final: 0.8913 (p) REVERT: P 67 MET cc_start: 0.8360 (ppp) cc_final: 0.7898 (ppp) REVERT: Q 30 PHE cc_start: 0.8393 (m-80) cc_final: 0.8046 (m-80) REVERT: Q 35 ASN cc_start: 0.8713 (m-40) cc_final: 0.7644 (m-40) REVERT: Q 44 LYS cc_start: 0.7333 (pttm) cc_final: 0.7048 (tmtt) REVERT: Q 64 PHE cc_start: 0.7584 (m-80) cc_final: 0.7267 (m-10) REVERT: S 2 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7863 (pm20) REVERT: S 39 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6339 (tpt170) REVERT: S 66 LEU cc_start: 0.8764 (pt) cc_final: 0.8303 (pt) REVERT: T 57 LEU cc_start: 0.7640 (mp) cc_final: 0.7390 (mt) REVERT: 8 17 PHE cc_start: 0.7542 (t80) cc_final: 0.7337 (t80) REVERT: 8 37 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7059 (mtp-110) REVERT: X 72 MET cc_start: 0.9039 (tmm) cc_final: 0.8489 (tmm) REVERT: X 180 ASN cc_start: 0.5958 (m-40) cc_final: 0.5749 (m-40) REVERT: X 237 LEU cc_start: 0.8667 (mp) cc_final: 0.8187 (mp) REVERT: 7 157 LYS cc_start: 0.5493 (mtmt) cc_final: 0.4662 (mtmt) REVERT: U 52 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7426 (mttt) REVERT: J 27 MET cc_start: 0.8422 (tpp) cc_final: 0.8184 (mmp) outliers start: 3 outliers final: 0 residues processed: 480 average time/residue: 0.0784 time to fit residues: 54.4707 Evaluate side-chains 402 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111314 restraints weight = 25188.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.113443 restraints weight = 16762.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114892 restraints weight = 12110.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.115539 restraints weight = 9580.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.116391 restraints weight = 8296.074| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9341 Z= 0.163 Angle : 0.826 10.549 12654 Z= 0.391 Chirality : 0.045 0.313 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.930 54.374 1276 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.22 % Allowed : 5.27 % Favored : 94.51 % 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: -1.90 (0.23), residues: 1192 helix: -0.84 (0.16), residues: 979 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 39 TYR 0.013 0.001 TYR U 82 PHE 0.029 0.002 PHE X 224 TRP 0.014 0.001 TRP X 234 HIS 0.003 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9341) covalent geometry : angle 0.82603 (12654) hydrogen bonds : bond 0.04300 ( 686) hydrogen bonds : angle 4.85678 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7953 (mp) cc_final: 0.7471 (tp) REVERT: K 39 ARG cc_start: 0.7767 (ptm-80) cc_final: 0.7558 (ttp80) REVERT: K 52 ILE cc_start: 0.9104 (mm) cc_final: 0.8845 (mm) REVERT: L 39 ARG cc_start: 0.7620 (ptm-80) cc_final: 0.6632 (tmt-80) REVERT: M 39 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.6900 (tpm170) REVERT: M 67 MET cc_start: 0.7592 (ppp) cc_final: 0.7363 (ppp) REVERT: N 53 LEU cc_start: 0.7964 (tt) cc_final: 0.7615 (mt) REVERT: N 59 GLU cc_start: 0.8338 (tp30) cc_final: 0.8113 (tp30) REVERT: P 24 ILE cc_start: 0.9359 (mt) cc_final: 0.9061 (mt) REVERT: P 59 GLU cc_start: 0.7999 (tp30) cc_final: 0.7722 (tp30) REVERT: P 67 MET cc_start: 0.8210 (ppp) cc_final: 0.7716 (ppp) REVERT: Q 30 PHE cc_start: 0.8248 (m-80) cc_final: 0.7837 (m-80) REVERT: Q 64 PHE cc_start: 0.7392 (m-80) cc_final: 0.7102 (m-10) REVERT: R 4 VAL cc_start: 0.8623 (m) cc_final: 0.8346 (p) REVERT: R 47 VAL cc_start: 0.9207 (t) cc_final: 0.8892 (p) REVERT: S 2 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7786 (pm20) REVERT: S 39 ARG cc_start: 0.7139 (ptm160) cc_final: 0.6429 (tpt170) REVERT: S 57 LEU cc_start: 0.8691 (mt) cc_final: 0.8353 (mt) REVERT: S 66 LEU cc_start: 0.8630 (pt) cc_final: 0.8397 (pt) REVERT: T 67 MET cc_start: 0.7727 (tmm) cc_final: 0.7280 (tmm) REVERT: X 70 MET cc_start: 0.7077 (tpt) cc_final: 0.6739 (tpt) REVERT: X 71 ASN cc_start: 0.8263 (m-40) cc_final: 0.8061 (m-40) REVERT: X 72 MET cc_start: 0.8766 (tmm) cc_final: 0.8555 (tmm) REVERT: X 88 MET cc_start: 0.8179 (ttm) cc_final: 0.7897 (ttm) REVERT: X 221 MET cc_start: 0.7896 (mtm) cc_final: 0.7670 (mtp) REVERT: 7 151 GLU cc_start: 0.7437 (pp20) cc_final: 0.6549 (tp30) REVERT: U 52 LYS cc_start: 0.7746 (ttpp) cc_final: 0.7479 (mttt) REVERT: U 73 ILE cc_start: 0.5590 (mt) cc_final: 0.5169 (mt) REVERT: U 76 PHE cc_start: 0.6813 (t80) cc_final: 0.6223 (m-80) REVERT: J 27 MET cc_start: 0.8536 (tpp) cc_final: 0.8253 (mmp) outliers start: 2 outliers final: 0 residues processed: 475 average time/residue: 0.0787 time to fit residues: 53.7784 Evaluate side-chains 392 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.128744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108950 restraints weight = 25688.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.111022 restraints weight = 16785.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112433 restraints weight = 12141.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.113215 restraints weight = 9617.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.113986 restraints weight = 8268.754| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9341 Z= 0.185 Angle : 0.813 10.112 12654 Z= 0.390 Chirality : 0.045 0.351 1558 Planarity : 0.004 0.062 1537 Dihedral : 5.779 54.933 1276 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -1.40 (0.24), residues: 1192 helix: -0.51 (0.16), residues: 982 sheet: None (None), residues: 0 loop : -2.25 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 39 TYR 0.021 0.002 TYR O 9 PHE 0.025 0.002 PHE P 64 TRP 0.016 0.001 TRP X 234 HIS 0.003 0.001 HIS X 114 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9341) covalent geometry : angle 0.81341 (12654) hydrogen bonds : bond 0.04143 ( 686) hydrogen bonds : angle 4.74234 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8099 (mp) cc_final: 0.7598 (tp) REVERT: K 52 ILE cc_start: 0.9034 (mm) cc_final: 0.8712 (mm) REVERT: L 39 ARG cc_start: 0.7733 (ptm-80) cc_final: 0.6524 (tmt-80) REVERT: M 67 MET cc_start: 0.7617 (ppp) cc_final: 0.7210 (ppp) REVERT: N 53 LEU cc_start: 0.8002 (tt) cc_final: 0.7529 (mt) REVERT: N 59 GLU cc_start: 0.8408 (tp30) cc_final: 0.8173 (tp30) REVERT: P 24 ILE cc_start: 0.9332 (mt) cc_final: 0.9073 (mm) REVERT: P 59 GLU cc_start: 0.8126 (tp30) cc_final: 0.7827 (tp30) REVERT: P 67 MET cc_start: 0.8080 (ppp) cc_final: 0.7530 (ppp) REVERT: R 4 VAL cc_start: 0.8645 (m) cc_final: 0.8359 (p) REVERT: R 47 VAL cc_start: 0.9385 (t) cc_final: 0.9021 (p) REVERT: S 2 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7790 (pm20) REVERT: S 39 ARG cc_start: 0.7457 (ptm160) cc_final: 0.6494 (tpt170) REVERT: T 67 MET cc_start: 0.7835 (tmm) cc_final: 0.7336 (tmm) REVERT: T 72 LEU cc_start: 0.8801 (tp) cc_final: 0.8573 (tp) REVERT: X 70 MET cc_start: 0.7347 (tpt) cc_final: 0.6987 (tpt) REVERT: X 221 MET cc_start: 0.7896 (mtm) cc_final: 0.7616 (mtp) REVERT: 7 151 GLU cc_start: 0.7440 (pp20) cc_final: 0.6912 (tp30) REVERT: 7 152 MET cc_start: 0.7106 (tmm) cc_final: 0.6609 (tmm) REVERT: U 52 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7540 (mttt) REVERT: J 27 MET cc_start: 0.8565 (tpp) cc_final: 0.8356 (mmp) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.0756 time to fit residues: 50.3357 Evaluate side-chains 385 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.0370 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 HIS U 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.131187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.111178 restraints weight = 25295.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.113315 restraints weight = 16677.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114709 restraints weight = 12170.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.115550 restraints weight = 9651.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.116276 restraints weight = 8316.938| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9341 Z= 0.159 Angle : 0.814 11.365 12654 Z= 0.384 Chirality : 0.044 0.298 1558 Planarity : 0.004 0.062 1537 Dihedral : 5.619 52.452 1276 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -1.22 (0.24), residues: 1192 helix: -0.39 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -2.61 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 169 TYR 0.020 0.001 TYR O 9 PHE 0.045 0.002 PHE Q 64 TRP 0.010 0.001 TRP X 234 HIS 0.001 0.000 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9341) covalent geometry : angle 0.81372 (12654) hydrogen bonds : bond 0.03930 ( 686) hydrogen bonds : angle 4.63062 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8107 (mp) cc_final: 0.7630 (tp) REVERT: K 52 ILE cc_start: 0.9019 (mm) cc_final: 0.8709 (mm) REVERT: M 67 MET cc_start: 0.7724 (ppp) cc_final: 0.7310 (ppp) REVERT: N 53 LEU cc_start: 0.7813 (tt) cc_final: 0.7437 (mt) REVERT: P 67 MET cc_start: 0.7965 (ppp) cc_final: 0.7448 (ppp) REVERT: Q 14 ILE cc_start: 0.9195 (mp) cc_final: 0.8982 (mp) REVERT: Q 30 PHE cc_start: 0.8198 (m-80) cc_final: 0.7835 (m-80) REVERT: Q 35 ASN cc_start: 0.8278 (m-40) cc_final: 0.7844 (m110) REVERT: Q 64 PHE cc_start: 0.7781 (m-80) cc_final: 0.7419 (m-80) REVERT: R 4 VAL cc_start: 0.8620 (m) cc_final: 0.8339 (p) REVERT: R 34 ILE cc_start: 0.9477 (mm) cc_final: 0.9232 (mm) REVERT: R 47 VAL cc_start: 0.9266 (t) cc_final: 0.8879 (p) REVERT: S 2 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7776 (pp30) REVERT: S 30 PHE cc_start: 0.7306 (m-80) cc_final: 0.7037 (m-10) REVERT: S 39 ARG cc_start: 0.7584 (ptm160) cc_final: 0.6522 (tpt170) REVERT: 8 12 GLN cc_start: 0.7249 (tt0) cc_final: 0.6917 (tt0) REVERT: X 67 ASP cc_start: 0.9073 (m-30) cc_final: 0.8828 (m-30) REVERT: X 70 MET cc_start: 0.7266 (tpt) cc_final: 0.6918 (tpt) REVERT: X 72 MET cc_start: 0.8938 (tmm) cc_final: 0.8651 (tmm) REVERT: X 88 MET cc_start: 0.8467 (ttm) cc_final: 0.8247 (ttm) REVERT: X 221 MET cc_start: 0.7587 (mtm) cc_final: 0.7203 (mtp) REVERT: 7 142 LYS cc_start: 0.8387 (tptp) cc_final: 0.7606 (tptp) REVERT: 7 151 GLU cc_start: 0.7488 (pp20) cc_final: 0.6998 (tp30) REVERT: 7 152 MET cc_start: 0.7347 (tmm) cc_final: 0.7065 (tmm) REVERT: U 52 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7383 (mttt) REVERT: U 76 PHE cc_start: 0.5999 (t80) cc_final: 0.5419 (m-80) REVERT: J 27 MET cc_start: 0.8525 (tpp) cc_final: 0.8300 (mmp) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.0776 time to fit residues: 51.2272 Evaluate side-chains 388 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.128251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108264 restraints weight = 26263.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110401 restraints weight = 17128.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.111741 restraints weight = 12396.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.112738 restraints weight = 9818.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113511 restraints weight = 8247.331| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9341 Z= 0.179 Angle : 0.830 11.456 12654 Z= 0.393 Chirality : 0.044 0.180 1558 Planarity : 0.004 0.060 1537 Dihedral : 5.591 52.948 1276 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -1.10 (0.24), residues: 1192 helix: -0.31 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.62 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 169 TYR 0.016 0.002 TYR O 9 PHE 0.034 0.002 PHE Q 64 TRP 0.027 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9341) covalent geometry : angle 0.83031 (12654) hydrogen bonds : bond 0.03922 ( 686) hydrogen bonds : angle 4.64737 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8094 (mp) cc_final: 0.7687 (tp) REVERT: K 52 ILE cc_start: 0.9040 (mm) cc_final: 0.8806 (mm) REVERT: L 39 ARG cc_start: 0.5491 (ptm160) cc_final: 0.4423 (tmt-80) REVERT: M 67 MET cc_start: 0.7690 (ppp) cc_final: 0.7364 (ppp) REVERT: N 53 LEU cc_start: 0.7767 (tt) cc_final: 0.7363 (mt) REVERT: P 67 MET cc_start: 0.8044 (ppp) cc_final: 0.7539 (ppp) REVERT: Q 14 ILE cc_start: 0.9237 (mp) cc_final: 0.8983 (mp) REVERT: Q 30 PHE cc_start: 0.8264 (m-80) cc_final: 0.7999 (m-80) REVERT: Q 35 ASN cc_start: 0.8222 (m-40) cc_final: 0.7751 (m-40) REVERT: Q 61 THR cc_start: 0.8986 (p) cc_final: 0.8764 (p) REVERT: Q 64 PHE cc_start: 0.7673 (m-80) cc_final: 0.7448 (m-80) REVERT: R 4 VAL cc_start: 0.8600 (m) cc_final: 0.8325 (p) REVERT: R 47 VAL cc_start: 0.9380 (t) cc_final: 0.9017 (p) REVERT: S 2 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7536 (pp30) REVERT: S 39 ARG cc_start: 0.7647 (ptm160) cc_final: 0.6415 (tpt170) REVERT: 8 12 GLN cc_start: 0.7625 (tt0) cc_final: 0.7172 (tt0) REVERT: X 67 ASP cc_start: 0.9046 (m-30) cc_final: 0.8768 (m-30) REVERT: X 70 MET cc_start: 0.7329 (tpt) cc_final: 0.6961 (tpt) REVERT: X 180 ASN cc_start: 0.5997 (m-40) cc_final: 0.5638 (m-40) REVERT: X 221 MET cc_start: 0.8089 (mtm) cc_final: 0.7509 (mtp) REVERT: 7 151 GLU cc_start: 0.7651 (pp20) cc_final: 0.6946 (tp30) REVERT: 7 152 MET cc_start: 0.7321 (tmm) cc_final: 0.6882 (tmm) REVERT: U 52 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7478 (mttt) REVERT: J 27 MET cc_start: 0.8471 (tpp) cc_final: 0.7988 (tpt) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.0744 time to fit residues: 47.6257 Evaluate side-chains 379 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.128647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109782 restraints weight = 26334.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111776 restraints weight = 17005.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.113045 restraints weight = 12330.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.113916 restraints weight = 9880.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114671 restraints weight = 8430.439| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9341 Z= 0.169 Angle : 0.832 11.035 12654 Z= 0.391 Chirality : 0.044 0.297 1558 Planarity : 0.004 0.059 1537 Dihedral : 5.472 52.899 1276 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -0.75 (0.24), residues: 1192 helix: -0.10 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -2.02 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 39 TYR 0.022 0.002 TYR L 9 PHE 0.029 0.002 PHE Q 64 TRP 0.009 0.001 TRP X 58 HIS 0.003 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9341) covalent geometry : angle 0.83156 (12654) hydrogen bonds : bond 0.03820 ( 686) hydrogen bonds : angle 4.56742 ( 2043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8078 (mp) cc_final: 0.7690 (tp) REVERT: K 52 ILE cc_start: 0.9098 (mm) cc_final: 0.8813 (mm) REVERT: L 39 ARG cc_start: 0.5196 (ptm160) cc_final: 0.4060 (tmt-80) REVERT: L 67 MET cc_start: 0.7301 (mmt) cc_final: 0.7071 (mmt) REVERT: M 67 MET cc_start: 0.7749 (ppp) cc_final: 0.7358 (ppp) REVERT: N 53 LEU cc_start: 0.7595 (tt) cc_final: 0.7301 (mt) REVERT: P 67 MET cc_start: 0.8252 (ppp) cc_final: 0.7686 (ppp) REVERT: Q 30 PHE cc_start: 0.8316 (m-80) cc_final: 0.7936 (m-80) REVERT: Q 35 ASN cc_start: 0.8181 (m-40) cc_final: 0.6888 (m-40) REVERT: Q 61 THR cc_start: 0.8963 (p) cc_final: 0.8751 (p) REVERT: Q 64 PHE cc_start: 0.7626 (m-80) cc_final: 0.7376 (m-80) REVERT: R 4 VAL cc_start: 0.8667 (m) cc_final: 0.8420 (p) REVERT: R 47 VAL cc_start: 0.9282 (t) cc_final: 0.8966 (p) REVERT: R 59 GLU cc_start: 0.8958 (pt0) cc_final: 0.8742 (pt0) REVERT: S 39 ARG cc_start: 0.7651 (ptm160) cc_final: 0.6445 (tpt170) REVERT: S 61 THR cc_start: 0.7349 (t) cc_final: 0.7128 (t) REVERT: S 64 PHE cc_start: 0.7459 (m-10) cc_final: 0.7029 (m-10) REVERT: 8 12 GLN cc_start: 0.7581 (tt0) cc_final: 0.7012 (tt0) REVERT: X 67 ASP cc_start: 0.8989 (m-30) cc_final: 0.8719 (m-30) REVERT: X 70 MET cc_start: 0.7226 (tpt) cc_final: 0.6996 (tpt) REVERT: X 176 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7788 (ttm-80) REVERT: X 180 ASN cc_start: 0.6450 (m-40) cc_final: 0.5945 (m-40) REVERT: X 221 MET cc_start: 0.8004 (mtm) cc_final: 0.7610 (mtp) REVERT: U 76 PHE cc_start: 0.5964 (t80) cc_final: 0.5461 (m-80) REVERT: J 27 MET cc_start: 0.8386 (tpp) cc_final: 0.7914 (tpt) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.0756 time to fit residues: 48.2905 Evaluate side-chains 375 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 12 GLN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.129464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109651 restraints weight = 26411.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.111829 restraints weight = 17248.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.113326 restraints weight = 12364.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114222 restraints weight = 9746.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.115024 restraints weight = 8282.077| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9341 Z= 0.159 Angle : 0.852 12.118 12654 Z= 0.394 Chirality : 0.045 0.272 1558 Planarity : 0.004 0.059 1537 Dihedral : 5.427 51.540 1276 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: -0.64 (0.25), residues: 1192 helix: -0.01 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -2.39 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 169 TYR 0.012 0.001 TYR U 51 PHE 0.032 0.002 PHE X 224 TRP 0.025 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9341) covalent geometry : angle 0.85206 (12654) hydrogen bonds : bond 0.03769 ( 686) hydrogen bonds : angle 4.54311 ( 2043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 52 ILE cc_start: 0.9123 (mm) cc_final: 0.8839 (mm) REVERT: L 39 ARG cc_start: 0.5244 (ptm160) cc_final: 0.4023 (tmt-80) REVERT: L 67 MET cc_start: 0.7577 (mmt) cc_final: 0.7280 (mmt) REVERT: M 9 TYR cc_start: 0.7836 (m-10) cc_final: 0.7557 (m-10) REVERT: M 67 MET cc_start: 0.7573 (ppp) cc_final: 0.7179 (ppp) REVERT: P 67 MET cc_start: 0.8268 (ppp) cc_final: 0.7687 (ppp) REVERT: Q 30 PHE cc_start: 0.8282 (m-80) cc_final: 0.8014 (m-80) REVERT: Q 35 ASN cc_start: 0.8104 (m-40) cc_final: 0.7349 (m-40) REVERT: Q 61 THR cc_start: 0.9004 (p) cc_final: 0.8773 (p) REVERT: Q 64 PHE cc_start: 0.7678 (m-80) cc_final: 0.7433 (m-80) REVERT: R 4 VAL cc_start: 0.8691 (m) cc_final: 0.8456 (p) REVERT: R 34 ILE cc_start: 0.9505 (mm) cc_final: 0.9303 (mm) REVERT: R 47 VAL cc_start: 0.9351 (t) cc_final: 0.8990 (p) REVERT: S 39 ARG cc_start: 0.7772 (ptm160) cc_final: 0.6377 (tpt170) REVERT: 8 12 GLN cc_start: 0.7602 (tt0) cc_final: 0.7105 (tt0) REVERT: X 67 ASP cc_start: 0.9047 (m-30) cc_final: 0.8660 (m-30) REVERT: X 70 MET cc_start: 0.7357 (tpt) cc_final: 0.7153 (tpt) REVERT: X 88 MET cc_start: 0.8209 (ttm) cc_final: 0.7999 (ttm) REVERT: X 176 ARG cc_start: 0.8399 (ttm110) cc_final: 0.7971 (ttm-80) REVERT: X 180 ASN cc_start: 0.6184 (m-40) cc_final: 0.5717 (m-40) REVERT: X 221 MET cc_start: 0.7949 (mtm) cc_final: 0.7572 (mtp) REVERT: Z 72 TYR cc_start: 0.7059 (t80) cc_final: 0.6527 (t80) REVERT: U 76 PHE cc_start: 0.6030 (t80) cc_final: 0.5461 (m-80) REVERT: J 27 MET cc_start: 0.8439 (tpp) cc_final: 0.7987 (tpt) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.0739 time to fit residues: 46.9006 Evaluate side-chains 375 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.127714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108358 restraints weight = 26296.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110229 restraints weight = 16981.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111614 restraints weight = 12823.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112476 restraints weight = 10222.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.113227 restraints weight = 8748.725| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9341 Z= 0.189 Angle : 0.870 14.436 12654 Z= 0.410 Chirality : 0.045 0.239 1558 Planarity : 0.004 0.058 1537 Dihedral : 5.510 52.416 1276 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -0.62 (0.24), residues: 1192 helix: -0.01 (0.16), residues: 1022 sheet: None (None), residues: 0 loop : -2.13 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 39 TYR 0.021 0.002 TYR O 9 PHE 0.032 0.002 PHE J 16 TRP 0.008 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9341) covalent geometry : angle 0.86960 (12654) hydrogen bonds : bond 0.03892 ( 686) hydrogen bonds : angle 4.60016 ( 2043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 52 ILE cc_start: 0.9183 (mm) cc_final: 0.8888 (mm) REVERT: L 39 ARG cc_start: 0.5152 (ptm160) cc_final: 0.4091 (tmt-80) REVERT: L 67 MET cc_start: 0.7249 (mmt) cc_final: 0.7028 (mmt) REVERT: M 9 TYR cc_start: 0.7835 (m-10) cc_final: 0.7476 (m-10) REVERT: M 67 MET cc_start: 0.7606 (ppp) cc_final: 0.7206 (ppp) REVERT: P 67 MET cc_start: 0.8317 (ppp) cc_final: 0.7687 (ppp) REVERT: Q 64 PHE cc_start: 0.7691 (m-80) cc_final: 0.7461 (m-80) REVERT: R 4 VAL cc_start: 0.8704 (m) cc_final: 0.8487 (p) REVERT: R 47 VAL cc_start: 0.9388 (t) cc_final: 0.9107 (p) REVERT: S 39 ARG cc_start: 0.7970 (ptm160) cc_final: 0.6478 (tpt170) REVERT: S 47 VAL cc_start: 0.9300 (t) cc_final: 0.8945 (t) REVERT: T 52 ILE cc_start: 0.6840 (mm) cc_final: 0.6637 (mm) REVERT: T 72 LEU cc_start: 0.8741 (tp) cc_final: 0.8507 (tp) REVERT: 8 12 GLN cc_start: 0.8096 (tt0) cc_final: 0.7844 (tt0) REVERT: X 67 ASP cc_start: 0.9061 (m-30) cc_final: 0.8678 (m-30) REVERT: X 70 MET cc_start: 0.7318 (tpt) cc_final: 0.7118 (tpt) REVERT: X 176 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7701 (ttm-80) REVERT: X 197 ASN cc_start: 0.6970 (t0) cc_final: 0.6630 (m110) REVERT: X 221 MET cc_start: 0.8015 (mtm) cc_final: 0.7764 (mtp) REVERT: Z 72 TYR cc_start: 0.7094 (t80) cc_final: 0.6498 (t80) REVERT: 7 169 ASN cc_start: 0.7799 (t0) cc_final: 0.7505 (t0) REVERT: U 76 PHE cc_start: 0.6023 (t80) cc_final: 0.5510 (m-80) REVERT: J 27 MET cc_start: 0.8512 (tpp) cc_final: 0.8038 (tpt) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.0719 time to fit residues: 45.5252 Evaluate side-chains 369 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 169 ASN U 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.130894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110967 restraints weight = 25766.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112899 restraints weight = 17821.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114069 restraints weight = 12760.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.114894 restraints weight = 10372.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115009 restraints weight = 8853.727| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 9341 Z= 0.159 Angle : 0.869 14.813 12654 Z= 0.403 Chirality : 0.046 0.376 1558 Planarity : 0.004 0.058 1537 Dihedral : 5.458 49.268 1276 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.48 (0.24), residues: 1192 helix: 0.10 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -2.29 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 39 TYR 0.021 0.002 TYR K 9 PHE 0.027 0.002 PHE X 224 TRP 0.014 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9341) covalent geometry : angle 0.86925 (12654) hydrogen bonds : bond 0.03745 ( 686) hydrogen bonds : angle 4.52191 ( 2043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 52 ILE cc_start: 0.9304 (mm) cc_final: 0.9001 (mm) REVERT: L 39 ARG cc_start: 0.5079 (ptm160) cc_final: 0.3999 (tmt-80) REVERT: M 9 TYR cc_start: 0.7840 (m-10) cc_final: 0.7526 (m-10) REVERT: M 67 MET cc_start: 0.7998 (ppp) cc_final: 0.7510 (ppp) REVERT: O 26 ILE cc_start: 0.8614 (pt) cc_final: 0.8409 (pt) REVERT: P 67 MET cc_start: 0.8226 (ppp) cc_final: 0.7622 (ppp) REVERT: Q 30 PHE cc_start: 0.8313 (m-80) cc_final: 0.8064 (m-80) REVERT: Q 61 THR cc_start: 0.9036 (p) cc_final: 0.8814 (p) REVERT: R 4 VAL cc_start: 0.8697 (m) cc_final: 0.8452 (p) REVERT: R 47 VAL cc_start: 0.9374 (t) cc_final: 0.9015 (p) REVERT: S 39 ARG cc_start: 0.8016 (ptm160) cc_final: 0.6469 (tpt170) REVERT: T 52 ILE cc_start: 0.6825 (mm) cc_final: 0.6602 (mm) REVERT: X 67 ASP cc_start: 0.9020 (m-30) cc_final: 0.8623 (m-30) REVERT: X 176 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7931 (ttm-80) REVERT: X 221 MET cc_start: 0.7869 (mtm) cc_final: 0.7516 (mtp) REVERT: Z 72 TYR cc_start: 0.7168 (t80) cc_final: 0.6573 (t80) REVERT: 7 144 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6562 (tm-30) REVERT: U 76 PHE cc_start: 0.6073 (t80) cc_final: 0.5534 (m-80) REVERT: J 27 MET cc_start: 0.8401 (tpp) cc_final: 0.7820 (tmm) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.0714 time to fit residues: 45.3411 Evaluate side-chains 373 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 12 GLN U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.130864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.110831 restraints weight = 25502.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112710 restraints weight = 16801.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114262 restraints weight = 12699.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115269 restraints weight = 10016.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.115707 restraints weight = 8405.014| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9341 Z= 0.157 Angle : 0.889 14.896 12654 Z= 0.411 Chirality : 0.046 0.266 1558 Planarity : 0.004 0.058 1537 Dihedral : 5.440 45.837 1276 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.52 (0.24), residues: 1192 helix: 0.05 (0.16), residues: 1046 sheet: None (None), residues: 0 loop : -2.37 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 39 TYR 0.014 0.001 TYR J 24 PHE 0.026 0.002 PHE O 64 TRP 0.014 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9341) covalent geometry : angle 0.88948 (12654) hydrogen bonds : bond 0.03767 ( 686) hydrogen bonds : angle 4.54089 ( 2043) =============================================================================== Job complete usr+sys time: 1679.89 seconds wall clock time: 29 minutes 42.32 seconds (1782.32 seconds total)