Starting phenix.real_space_refine on Thu Mar 13 11:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cp7_7549/03_2025/6cp7_7549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp7_7549/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6cp7_7549/03_2025/6cp7_7549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp7_7549/03_2025/6cp7_7549.map" model { file = "/net/cci-nas-00/data/ceres_data/6cp7_7549/03_2025/6cp7_7549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp7_7549/03_2025/6cp7_7549.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'ARG:plan': 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: 6.35, per 1000 atoms: 0.69 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.78 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: 2.38 Time building geometry restraints manager: 2.92 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: 3.900 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.940 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.040 ------------------------------------------------------------------------------- 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= 0.521 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP X 234 HIS 0.012 0.003 HIS X 114 PHE 0.034 0.004 PHE X 224 TYR 0.026 0.003 TYR U 51 ARG 0.011 0.001 ARG X 176 *********************** 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 : 1.030 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: 0.8968 (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: 0.8259 (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: 0.5902 (tpt170) REVERT: S 66 LEU cc_start: 0.8009 (pt) cc_final: 0.7803 (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: 0.5017 (mm) REVERT: X 53 ILE cc_start: 0.5247 (mt) cc_final: 0.5030 (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: 0.2112 time to fit residues: 159.8464 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 : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN U 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.129076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108716 restraints weight = 25268.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.111001 restraints weight = 15627.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.112489 restraints weight = 11073.476| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9341 Z= 0.279 Angle : 0.892 11.015 12654 Z= 0.431 Chirality : 0.046 0.286 1558 Planarity : 0.006 0.060 1537 Dihedral : 6.649 58.839 1276 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.43 % Allowed : 5.92 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.21), residues: 1192 helix: -1.65 (0.14), residues: 983 sheet: None (None), residues: 0 loop : -2.77 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 234 HIS 0.007 0.002 HIS X 185 PHE 0.032 0.002 PHE K 55 TYR 0.033 0.002 TYR X 241 ARG 0.011 0.001 ARG U 50 *********************** 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 477 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 473 time to evaluate : 0.924 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: 0.7825 (mp) cc_final: 0.7339 (tp) REVERT: K 64 PHE cc_start: 0.7666 (m-10) cc_final: 0.7273 (m-10) REVERT: L 39 ARG cc_start: 0.7705 (ptm-80) cc_final: 0.6577 (tmt-80) REVERT: L 47 VAL cc_start: 0.9021 (t) cc_final: 0.8690 (p) REVERT: L 71 LEU cc_start: 0.8339 (pp) cc_final: 0.8102 (pp) REVERT: M 4 VAL cc_start: 0.7189 (p) cc_final: 0.6987 (m) REVERT: M 39 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.6761 (tpm170) REVERT: M 58 SER cc_start: 0.8849 (m) cc_final: 0.8568 (p) REVERT: N 53 LEU cc_start: 0.8300 (tt) cc_final: 0.7729 (mt) REVERT: O 35 ASN cc_start: 0.8520 (t0) cc_final: 0.8283 (t0) REVERT: O 64 PHE cc_start: 0.7700 (m-10) cc_final: 0.7418 (m-10) REVERT: O 66 LEU cc_start: 0.8581 (pt) cc_final: 0.8374 (tt) REVERT: P 58 SER cc_start: 0.9202 (t) cc_final: 0.8997 (p) REVERT: P 67 MET cc_start: 0.8433 (ppp) cc_final: 0.7994 (ppp) REVERT: Q 64 PHE cc_start: 0.7691 (m-80) cc_final: 0.7287 (m-10) REVERT: S 2 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7893 (pm20) REVERT: S 39 ARG cc_start: 0.7255 (ptm160) cc_final: 0.6420 (tpt170) REVERT: S 66 LEU cc_start: 0.8786 (pt) cc_final: 0.8285 (pt) REVERT: T 57 LEU cc_start: 0.7749 (mp) cc_final: 0.7512 (mt) REVERT: X 72 MET cc_start: 0.9095 (tmm) cc_final: 0.8493 (tmm) REVERT: X 180 ASN cc_start: 0.6049 (m-40) cc_final: 0.5828 (m-40) REVERT: 7 151 GLU cc_start: 0.7633 (pp20) cc_final: 0.7058 (pp20) REVERT: J 27 MET cc_start: 0.8425 (tpp) cc_final: 0.8142 (mmp) outliers start: 4 outliers final: 1 residues processed: 475 average time/residue: 0.1853 time to fit residues: 124.8422 Evaluate side-chains 393 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.129769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.109701 restraints weight = 25438.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.111776 restraints weight = 16443.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113076 restraints weight = 11878.678| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4303 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= 0.235 Angle : 0.848 12.283 12654 Z= 0.397 Chirality : 0.045 0.353 1558 Planarity : 0.004 0.061 1537 Dihedral : 6.056 56.729 1276 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.22 % Allowed : 5.06 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.23), residues: 1192 helix: -0.90 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.035 0.002 PHE X 224 TYR 0.014 0.002 TYR U 55 ARG 0.002 0.000 ARG X 169 *********************** 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 471 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 0.933 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 5 LEU cc_start: 0.7772 (mp) cc_final: 0.7329 (tp) REVERT: L 39 ARG cc_start: 0.7704 (ptm-80) cc_final: 0.6769 (tmt-80) REVERT: L 47 VAL cc_start: 0.8894 (t) cc_final: 0.8556 (p) REVERT: L 66 LEU cc_start: 0.7350 (pt) cc_final: 0.6456 (mt) REVERT: M 39 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.6925 (tpm170) REVERT: M 67 MET cc_start: 0.7707 (ppp) cc_final: 0.7470 (ppp) REVERT: N 53 LEU cc_start: 0.8049 (tt) cc_final: 0.7606 (mt) REVERT: N 59 GLU cc_start: 0.8400 (tp30) cc_final: 0.8192 (tp30) REVERT: O 35 ASN cc_start: 0.8101 (t0) cc_final: 0.7822 (t0) REVERT: O 46 THR cc_start: 0.7858 (p) cc_final: 0.7645 (p) REVERT: P 24 ILE cc_start: 0.9361 (mt) cc_final: 0.9079 (mt) REVERT: P 59 GLU cc_start: 0.8146 (tp30) cc_final: 0.7806 (tp30) REVERT: P 67 MET cc_start: 0.8322 (ppp) cc_final: 0.7853 (ppp) REVERT: Q 30 PHE cc_start: 0.8276 (m-80) cc_final: 0.7925 (m-80) REVERT: Q 64 PHE cc_start: 0.7669 (m-80) cc_final: 0.7289 (m-10) REVERT: R 43 ILE cc_start: 0.8984 (tt) cc_final: 0.8777 (tt) REVERT: R 47 VAL cc_start: 0.9253 (t) cc_final: 0.8927 (p) REVERT: S 2 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7856 (pm20) REVERT: S 39 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6530 (tpt170) REVERT: S 57 LEU cc_start: 0.8760 (mt) cc_final: 0.8496 (mt) REVERT: T 67 MET cc_start: 0.7920 (tmm) cc_final: 0.7082 (tmm) REVERT: X 88 MET cc_start: 0.8123 (ttm) cc_final: 0.7810 (ttm) REVERT: 7 157 LYS cc_start: 0.4988 (mtpt) cc_final: 0.4440 (mtmt) REVERT: U 76 PHE cc_start: 0.6350 (t80) cc_final: 0.6114 (t80) REVERT: J 27 MET cc_start: 0.8500 (tpp) cc_final: 0.8224 (mmp) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.1802 time to fit residues: 120.8486 Evaluate side-chains 393 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 62 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.128212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109186 restraints weight = 25543.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111138 restraints weight = 16330.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.112434 restraints weight = 11928.859| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9341 Z= 0.261 Angle : 0.814 10.485 12654 Z= 0.391 Chirality : 0.045 0.359 1558 Planarity : 0.004 0.060 1537 Dihedral : 5.866 56.521 1276 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.23), residues: 1192 helix: -0.54 (0.16), residues: 983 sheet: None (None), residues: 0 loop : -2.29 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 234 HIS 0.003 0.001 HIS X 114 PHE 0.026 0.002 PHE T 70 TYR 0.019 0.002 TYR U 55 ARG 0.006 0.001 ARG Q 39 *********************** 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 456 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8102 (mp) cc_final: 0.7612 (tp) REVERT: L 39 ARG cc_start: 0.7939 (ptm-80) cc_final: 0.6858 (tmt-80) REVERT: M 67 MET cc_start: 0.7669 (ppp) cc_final: 0.7255 (ppp) REVERT: N 53 LEU cc_start: 0.7992 (tt) cc_final: 0.7515 (mt) REVERT: N 59 GLU cc_start: 0.8320 (tp30) cc_final: 0.8113 (tp30) REVERT: P 24 ILE cc_start: 0.9334 (mt) cc_final: 0.9062 (mt) REVERT: P 39 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7504 (mtp-110) REVERT: P 59 GLU cc_start: 0.8076 (tp30) cc_final: 0.7790 (tp30) REVERT: P 67 MET cc_start: 0.8144 (ppp) cc_final: 0.7617 (ppp) REVERT: Q 14 ILE cc_start: 0.9297 (mt) cc_final: 0.9048 (mp) REVERT: R 47 VAL cc_start: 0.9244 (t) cc_final: 0.8929 (p) REVERT: S 2 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7783 (pm20) REVERT: S 30 PHE cc_start: 0.7192 (m-80) cc_final: 0.6978 (m-10) REVERT: S 39 ARG cc_start: 0.7477 (ptm160) cc_final: 0.6542 (tpt170) REVERT: S 57 LEU cc_start: 0.8671 (mt) cc_final: 0.8456 (mt) REVERT: S 59 GLU cc_start: 0.7757 (tp30) cc_final: 0.7555 (tp30) REVERT: S 61 THR cc_start: 0.7473 (t) cc_final: 0.7266 (t) REVERT: S 64 PHE cc_start: 0.7395 (m-10) cc_final: 0.6908 (m-10) REVERT: T 67 MET cc_start: 0.7748 (tmm) cc_final: 0.7399 (tmm) REVERT: X 221 MET cc_start: 0.7843 (mtp) cc_final: 0.7275 (mtp) REVERT: 7 151 GLU cc_start: 0.7211 (pp20) cc_final: 0.6758 (tp30) REVERT: 7 157 LYS cc_start: 0.5724 (mtpt) cc_final: 0.5106 (tttm) REVERT: U 76 PHE cc_start: 0.6206 (t80) cc_final: 0.5480 (m-80) REVERT: J 27 MET cc_start: 0.8547 (tpp) cc_final: 0.8289 (mmp) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1804 time to fit residues: 117.7633 Evaluate side-chains 384 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 180 ASN U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.126708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.107304 restraints weight = 26050.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.109292 restraints weight = 16642.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110639 restraints weight = 12097.913| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9341 Z= 0.297 Angle : 0.847 11.910 12654 Z= 0.413 Chirality : 0.047 0.288 1558 Planarity : 0.005 0.063 1537 Dihedral : 5.881 58.378 1276 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1192 helix: -0.53 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.49 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.044 0.003 PHE Q 64 TYR 0.023 0.002 TYR X 32 ARG 0.007 0.001 ARG X 169 *********************** 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 439 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 438 time to evaluate : 0.977 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: 0.8155 (mp) cc_final: 0.7699 (tp) REVERT: L 39 ARG cc_start: 0.7937 (ptm-80) cc_final: 0.6709 (tmt-80) REVERT: M 67 MET cc_start: 0.7821 (ppp) cc_final: 0.7414 (ppp) REVERT: N 53 LEU cc_start: 0.8046 (tt) cc_final: 0.7717 (mt) REVERT: P 59 GLU cc_start: 0.8235 (tp30) cc_final: 0.7885 (tp30) REVERT: P 67 MET cc_start: 0.8176 (ppp) cc_final: 0.7703 (ppp) REVERT: Q 14 ILE cc_start: 0.9131 (mt) cc_final: 0.8883 (mp) REVERT: Q 35 ASN cc_start: 0.8450 (m-40) cc_final: 0.7714 (m-40) REVERT: Q 40 ASN cc_start: 0.8082 (t0) cc_final: 0.7793 (t0) REVERT: Q 64 PHE cc_start: 0.7900 (m-80) cc_final: 0.7565 (m-80) REVERT: R 4 VAL cc_start: 0.8615 (m) cc_final: 0.8308 (p) REVERT: R 47 VAL cc_start: 0.9341 (t) cc_final: 0.8991 (p) REVERT: S 2 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7866 (pp30) REVERT: S 30 PHE cc_start: 0.7429 (m-80) cc_final: 0.7211 (m-10) REVERT: S 39 ARG cc_start: 0.7628 (ptm160) cc_final: 0.6409 (tpt170) REVERT: S 64 PHE cc_start: 0.7423 (m-10) cc_final: 0.7053 (m-10) REVERT: T 10 ILE cc_start: 0.8470 (tp) cc_final: 0.8076 (tt) REVERT: T 67 MET cc_start: 0.7861 (tmm) cc_final: 0.7553 (tmm) REVERT: X 67 ASP cc_start: 0.9152 (m-30) cc_final: 0.8872 (m-30) REVERT: X 88 MET cc_start: 0.8433 (ttm) cc_final: 0.8178 (ttm) REVERT: X 180 ASN cc_start: 0.6760 (m110) cc_final: 0.5756 (m110) REVERT: X 221 MET cc_start: 0.7765 (mtp) cc_final: 0.7200 (mtp) REVERT: 7 151 GLU cc_start: 0.7322 (pp20) cc_final: 0.6660 (tp30) REVERT: 7 152 MET cc_start: 0.6889 (tmm) cc_final: 0.6548 (tmm) REVERT: 7 157 LYS cc_start: 0.5814 (mtpt) cc_final: 0.5439 (tttt) outliers start: 1 outliers final: 1 residues processed: 439 average time/residue: 0.1763 time to fit residues: 110.7055 Evaluate side-chains 373 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 76 GLN ** 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 = 0.4064 r_free = 0.4064 target = 0.129390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.110253 restraints weight = 25426.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112280 restraints weight = 16407.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.113519 restraints weight = 11898.507| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9341 Z= 0.243 Angle : 0.827 12.510 12654 Z= 0.390 Chirality : 0.046 0.399 1558 Planarity : 0.004 0.063 1537 Dihedral : 5.675 55.611 1276 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1192 helix: -0.29 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.49 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.034 0.002 PHE Q 64 TYR 0.022 0.002 TYR M 9 ARG 0.003 0.000 ARG X 169 *********************** 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 444 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7932 (mp) cc_final: 0.7595 (tp) REVERT: L 39 ARG cc_start: 0.7752 (ptm-80) cc_final: 0.6660 (tmt-80) REVERT: M 45 ASP cc_start: 0.7769 (m-30) cc_final: 0.7542 (p0) REVERT: M 67 MET cc_start: 0.7711 (ppp) cc_final: 0.7341 (ppp) REVERT: N 53 LEU cc_start: 0.7997 (tt) cc_final: 0.7642 (mt) REVERT: P 59 GLU cc_start: 0.8069 (tp30) cc_final: 0.7815 (tp30) REVERT: P 67 MET cc_start: 0.8292 (ppp) cc_final: 0.7732 (ppp) REVERT: Q 14 ILE cc_start: 0.9151 (mt) cc_final: 0.8942 (mt) REVERT: Q 35 ASN cc_start: 0.8167 (m-40) cc_final: 0.7808 (m-40) REVERT: Q 40 ASN cc_start: 0.7880 (t0) cc_final: 0.7651 (t0) REVERT: Q 64 PHE cc_start: 0.7841 (m-80) cc_final: 0.7554 (m-80) REVERT: R 4 VAL cc_start: 0.8585 (m) cc_final: 0.8316 (p) REVERT: R 47 VAL cc_start: 0.9320 (t) cc_final: 0.8960 (p) REVERT: R 65 CYS cc_start: 0.7763 (t) cc_final: 0.7503 (t) REVERT: S 30 PHE cc_start: 0.7268 (m-80) cc_final: 0.7053 (m-10) REVERT: S 39 ARG cc_start: 0.7612 (ptm160) cc_final: 0.6406 (tpt170) REVERT: S 61 THR cc_start: 0.7306 (t) cc_final: 0.7070 (t) REVERT: S 64 PHE cc_start: 0.7290 (m-10) cc_final: 0.6938 (m-10) REVERT: T 67 MET cc_start: 0.7769 (tmm) cc_final: 0.6889 (tmm) REVERT: X 67 ASP cc_start: 0.9070 (m-30) cc_final: 0.8778 (m-30) REVERT: X 221 MET cc_start: 0.7832 (mtp) cc_final: 0.7238 (mtp) REVERT: 7 151 GLU cc_start: 0.7409 (pp20) cc_final: 0.6626 (tp30) REVERT: 7 152 MET cc_start: 0.6935 (tmm) cc_final: 0.6638 (tmm) REVERT: U 76 PHE cc_start: 0.6069 (t80) cc_final: 0.5528 (m-80) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1693 time to fit residues: 108.7032 Evaluate side-chains 387 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.129963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.110097 restraints weight = 26074.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112282 restraints weight = 16840.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.113789 restraints weight = 11949.855| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9341 Z= 0.239 Angle : 0.829 11.046 12654 Z= 0.389 Chirality : 0.048 0.459 1558 Planarity : 0.004 0.065 1537 Dihedral : 5.599 53.788 1276 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1192 helix: -0.08 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -2.42 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.030 0.002 PHE Q 64 TYR 0.023 0.002 TYR L 9 ARG 0.002 0.000 ARG Q 39 *********************** 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 442 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7843 (mp) cc_final: 0.7519 (tp) REVERT: L 39 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.6849 (tmt-80) REVERT: M 67 MET cc_start: 0.7855 (ppp) cc_final: 0.7454 (ppp) REVERT: N 53 LEU cc_start: 0.7820 (tt) cc_final: 0.7508 (mt) REVERT: O 5 LEU cc_start: 0.7671 (pt) cc_final: 0.7442 (mp) REVERT: O 55 PHE cc_start: 0.7724 (t80) cc_final: 0.7477 (t80) REVERT: P 67 MET cc_start: 0.8316 (ppp) cc_final: 0.7720 (ppp) REVERT: Q 35 ASN cc_start: 0.8205 (m-40) cc_final: 0.7758 (m-40) REVERT: Q 40 ASN cc_start: 0.8070 (t0) cc_final: 0.7844 (t0) REVERT: Q 64 PHE cc_start: 0.7785 (m-80) cc_final: 0.7510 (m-80) REVERT: R 4 VAL cc_start: 0.8624 (m) cc_final: 0.8341 (p) REVERT: R 47 VAL cc_start: 0.9321 (t) cc_final: 0.8952 (p) REVERT: S 30 PHE cc_start: 0.7355 (m-80) cc_final: 0.7109 (m-10) REVERT: S 39 ARG cc_start: 0.7614 (ptm160) cc_final: 0.6318 (tpt170) REVERT: S 61 THR cc_start: 0.7323 (t) cc_final: 0.7076 (t) REVERT: S 64 PHE cc_start: 0.7204 (m-10) cc_final: 0.6888 (m-10) REVERT: T 67 MET cc_start: 0.7682 (tmm) cc_final: 0.7418 (tmm) REVERT: X 67 ASP cc_start: 0.9037 (m-30) cc_final: 0.8684 (m-30) REVERT: X 221 MET cc_start: 0.7832 (mtp) cc_final: 0.7227 (mtp) REVERT: 7 142 LYS cc_start: 0.8419 (tptp) cc_final: 0.8061 (tptp) REVERT: 7 151 GLU cc_start: 0.7394 (pp20) cc_final: 0.6676 (tp30) REVERT: 7 152 MET cc_start: 0.7025 (tmm) cc_final: 0.6717 (tmm) REVERT: U 76 PHE cc_start: 0.5958 (t80) cc_final: 0.5484 (m-80) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1726 time to fit residues: 110.4772 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN ** X 71 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 = 0.129507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.110746 restraints weight = 26304.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112564 restraints weight = 17429.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.113678 restraints weight = 12325.066| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9341 Z= 0.259 Angle : 0.849 13.581 12654 Z= 0.398 Chirality : 0.048 0.478 1558 Planarity : 0.004 0.062 1537 Dihedral : 5.612 53.480 1276 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.11 % Allowed : 1.94 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1192 helix: -0.06 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.36 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 67 HIS 0.002 0.001 HIS X 137 PHE 0.028 0.002 PHE X 224 TYR 0.015 0.002 TYR U 51 ARG 0.003 0.000 ARG Q 39 *********************** 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 430 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 ARG cc_start: 0.7737 (ptm-80) cc_final: 0.6868 (tmt-80) REVERT: M 9 TYR cc_start: 0.8008 (m-10) cc_final: 0.7626 (m-10) REVERT: M 67 MET cc_start: 0.7913 (ppp) cc_final: 0.7487 (ppp) REVERT: N 53 LEU cc_start: 0.7957 (tt) cc_final: 0.7476 (mt) REVERT: O 5 LEU cc_start: 0.7787 (pt) cc_final: 0.7579 (mp) REVERT: O 55 PHE cc_start: 0.7734 (t80) cc_final: 0.7447 (t80) REVERT: P 67 MET cc_start: 0.8358 (ppp) cc_final: 0.7723 (ppp) REVERT: Q 35 ASN cc_start: 0.8167 (m-40) cc_final: 0.7098 (m-40) REVERT: Q 40 ASN cc_start: 0.8016 (t0) cc_final: 0.7789 (t0) REVERT: Q 64 PHE cc_start: 0.7861 (m-80) cc_final: 0.7605 (m-80) REVERT: R 4 VAL cc_start: 0.8645 (m) cc_final: 0.8383 (p) REVERT: R 47 VAL cc_start: 0.9307 (t) cc_final: 0.8957 (p) REVERT: S 30 PHE cc_start: 0.7284 (m-80) cc_final: 0.7036 (m-10) REVERT: S 39 ARG cc_start: 0.7626 (ptm160) cc_final: 0.6402 (tpt170) REVERT: S 61 THR cc_start: 0.7297 (t) cc_final: 0.7062 (t) REVERT: S 64 PHE cc_start: 0.7244 (m-10) cc_final: 0.6928 (m-10) REVERT: T 67 MET cc_start: 0.7805 (tmm) cc_final: 0.7517 (tmm) REVERT: X 67 ASP cc_start: 0.9018 (m-30) cc_final: 0.8741 (m-30) REVERT: X 176 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7666 (ttm-80) REVERT: X 221 MET cc_start: 0.7786 (mtp) cc_final: 0.7286 (mtp) REVERT: 7 151 GLU cc_start: 0.7397 (pp20) cc_final: 0.6656 (tp30) REVERT: 7 152 MET cc_start: 0.7224 (tmm) cc_final: 0.6920 (tmm) REVERT: U 76 PHE cc_start: 0.6023 (t80) cc_final: 0.5485 (m-80) outliers start: 1 outliers final: 0 residues processed: 429 average time/residue: 0.1730 time to fit residues: 106.3232 Evaluate side-chains 368 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** Z 93 ASN U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.130236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.110541 restraints weight = 25707.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112641 restraints weight = 16589.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113941 restraints weight = 12042.976| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9341 Z= 0.250 Angle : 0.863 11.889 12654 Z= 0.403 Chirality : 0.048 0.445 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.589 51.301 1276 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1192 helix: 0.00 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -2.15 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.028 0.002 PHE X 224 TYR 0.018 0.001 TYR L 9 ARG 0.002 0.000 ARG Q 39 *********************** 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 428 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 ARG cc_start: 0.7826 (ptm-80) cc_final: 0.6839 (tmt-80) REVERT: L 67 MET cc_start: 0.7637 (mmt) cc_final: 0.7348 (mmt) REVERT: M 9 TYR cc_start: 0.7948 (m-10) cc_final: 0.7550 (m-10) REVERT: M 67 MET cc_start: 0.7961 (ppp) cc_final: 0.7466 (ppp) REVERT: O 5 LEU cc_start: 0.7653 (pt) cc_final: 0.7415 (mp) REVERT: O 26 ILE cc_start: 0.8591 (pt) cc_final: 0.8252 (pt) REVERT: P 67 MET cc_start: 0.8310 (ppp) cc_final: 0.7688 (ppp) REVERT: Q 35 ASN cc_start: 0.8380 (m-40) cc_final: 0.7656 (m-40) REVERT: Q 40 ASN cc_start: 0.8138 (t0) cc_final: 0.7933 (t0) REVERT: Q 64 PHE cc_start: 0.7797 (m-80) cc_final: 0.7566 (m-80) REVERT: R 4 VAL cc_start: 0.8636 (m) cc_final: 0.8368 (p) REVERT: R 47 VAL cc_start: 0.9262 (t) cc_final: 0.8858 (p) REVERT: S 30 PHE cc_start: 0.7399 (m-80) cc_final: 0.7113 (m-10) REVERT: S 39 ARG cc_start: 0.7817 (ptm160) cc_final: 0.6400 (tpt170) REVERT: S 50 MET cc_start: 0.8009 (ptp) cc_final: 0.7790 (ptp) REVERT: T 63 LEU cc_start: 0.8530 (mm) cc_final: 0.8141 (mm) REVERT: T 67 MET cc_start: 0.7738 (tmm) cc_final: 0.7353 (tmm) REVERT: X 67 ASP cc_start: 0.9019 (m-30) cc_final: 0.8689 (m-30) REVERT: X 176 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7567 (ttm-80) REVERT: 7 151 GLU cc_start: 0.7418 (pp20) cc_final: 0.6651 (tp30) REVERT: 7 152 MET cc_start: 0.7066 (tmm) cc_final: 0.6843 (tmm) REVERT: 7 157 LYS cc_start: 0.7086 (tttt) cc_final: 0.6776 (tttm) REVERT: U 76 PHE cc_start: 0.6044 (t80) cc_final: 0.5512 (m-80) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.1756 time to fit residues: 109.4730 Evaluate side-chains 372 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.129649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.110199 restraints weight = 26222.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112410 restraints weight = 17271.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113924 restraints weight = 12311.091| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9341 Z= 0.241 Angle : 0.871 14.722 12654 Z= 0.403 Chirality : 0.047 0.404 1558 Planarity : 0.004 0.060 1537 Dihedral : 5.546 49.269 1276 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1192 helix: 0.06 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.31 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.029 0.002 PHE X 224 TYR 0.013 0.001 TYR S 9 ARG 0.002 0.000 ARG Q 39 ********************** 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 424 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.924 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: L 39 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.6827 (tmt-80) REVERT: M 9 TYR cc_start: 0.7871 (m-10) cc_final: 0.7506 (m-10) REVERT: M 67 MET cc_start: 0.7955 (ppp) cc_final: 0.7513 (ppp) REVERT: N 10 ILE cc_start: 0.8269 (tp) cc_final: 0.8048 (tp) REVERT: O 5 LEU cc_start: 0.7757 (pt) cc_final: 0.7506 (mp) REVERT: O 64 PHE cc_start: 0.7254 (m-10) cc_final: 0.7048 (m-80) REVERT: P 67 MET cc_start: 0.8297 (ppp) cc_final: 0.7660 (ppp) REVERT: Q 35 ASN cc_start: 0.8121 (m-40) cc_final: 0.7334 (m-40) REVERT: Q 61 THR cc_start: 0.9044 (p) cc_final: 0.8829 (p) REVERT: R 4 VAL cc_start: 0.8670 (m) cc_final: 0.8406 (p) REVERT: R 47 VAL cc_start: 0.9207 (t) cc_final: 0.8768 (p) REVERT: S 30 PHE cc_start: 0.7358 (m-80) cc_final: 0.7084 (m-10) REVERT: S 39 ARG cc_start: 0.7977 (ptm160) cc_final: 0.6476 (tpt170) REVERT: T 52 ILE cc_start: 0.6619 (mm) cc_final: 0.6386 (mm) REVERT: T 59 GLU cc_start: 0.8405 (tp30) cc_final: 0.7990 (tp30) REVERT: T 67 MET cc_start: 0.7765 (tmm) cc_final: 0.7463 (tmm) REVERT: 8 14 THR cc_start: 0.8074 (m) cc_final: 0.7864 (m) REVERT: X 67 ASP cc_start: 0.9081 (m-30) cc_final: 0.8713 (m-30) REVERT: X 70 MET cc_start: 0.7467 (tpt) cc_final: 0.7170 (tpt) REVERT: Z 86 LYS cc_start: 0.8706 (tptp) cc_final: 0.8329 (ttmm) REVERT: U 76 PHE cc_start: 0.6059 (t80) cc_final: 0.5526 (m-80) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.1695 time to fit residues: 103.7942 Evaluate side-chains 354 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.131439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.112043 restraints weight = 25782.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114052 restraints weight = 17010.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.115455 restraints weight = 12450.034| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9341 Z= 0.228 Angle : 0.876 14.256 12654 Z= 0.402 Chirality : 0.047 0.402 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.457 45.461 1276 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1192 helix: 0.13 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.27 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.027 0.002 PHE X 224 TYR 0.017 0.001 TYR L 9 ARG 0.001 0.000 ARG X 169 =============================================================================== Job complete usr+sys time: 3315.24 seconds wall clock time: 58 minutes 39.27 seconds (3519.27 seconds total)