Starting phenix.real_space_refine on Thu Feb 13 09:13:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cp7_7549/02_2025/6cp7_7549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp7_7549/02_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_7549/02_2025/6cp7_7549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp7_7549/02_2025/6cp7_7549.map" model { file = "/net/cci-nas-00/data/ceres_data/6cp7_7549/02_2025/6cp7_7549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp7_7549/02_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-5592/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: 6.21, per 1000 atoms: 0.68 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: 2.58 Conformation dependent library (CDL) restraints added in 1.4 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: 0.84 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: 2.57 Time building geometry restraints manager: 3.01 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: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.710 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- 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 : 0.955 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: 0.1885 time to fit residues: 142.0091 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 : 1.014 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.108772 restraints weight = 25268.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.110980 restraints weight = 15634.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112550 restraints weight = 11030.674| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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: 0.7822 (mp) cc_final: 0.7337 (tp) REVERT: K 64 PHE cc_start: 0.7663 (m-10) cc_final: 0.7270 (m-10) REVERT: L 39 ARG cc_start: 0.7704 (ptm-80) cc_final: 0.6575 (tmt-80) REVERT: L 47 VAL cc_start: 0.9024 (t) cc_final: 0.8691 (p) REVERT: L 71 LEU cc_start: 0.8336 (pp) cc_final: 0.8100 (pp) REVERT: M 4 VAL cc_start: 0.7192 (p) cc_final: 0.6990 (m) REVERT: M 39 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.6761 (tpm170) REVERT: M 58 SER cc_start: 0.8848 (m) cc_final: 0.8567 (p) REVERT: N 53 LEU cc_start: 0.8301 (tt) cc_final: 0.7730 (mt) REVERT: O 35 ASN cc_start: 0.8512 (t0) cc_final: 0.8275 (t0) REVERT: O 64 PHE cc_start: 0.7700 (m-10) cc_final: 0.7417 (m-10) REVERT: O 66 LEU cc_start: 0.8581 (pt) cc_final: 0.8374 (tt) REVERT: P 58 SER cc_start: 0.9203 (t) cc_final: 0.8997 (p) REVERT: P 67 MET cc_start: 0.8432 (ppp) cc_final: 0.7991 (ppp) REVERT: Q 64 PHE cc_start: 0.7684 (m-80) cc_final: 0.7279 (m-10) REVERT: S 2 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7890 (pm20) REVERT: S 39 ARG cc_start: 0.7260 (ptm160) cc_final: 0.6419 (tpt170) REVERT: S 57 LEU cc_start: 0.8653 (mt) cc_final: 0.8453 (mt) REVERT: S 66 LEU cc_start: 0.8786 (pt) cc_final: 0.8286 (pt) REVERT: T 57 LEU cc_start: 0.7748 (mp) cc_final: 0.7512 (mt) REVERT: X 72 MET cc_start: 0.9099 (tmm) cc_final: 0.8495 (tmm) REVERT: X 180 ASN cc_start: 0.6044 (m-40) cc_final: 0.5826 (m-40) REVERT: 7 151 GLU cc_start: 0.7633 (pp20) cc_final: 0.7059 (pp20) REVERT: J 27 MET cc_start: 0.8427 (tpp) cc_final: 0.8138 (mmp) outliers start: 4 outliers final: 1 residues processed: 475 average time/residue: 0.1928 time to fit residues: 129.6431 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 : 0.991 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.130149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.110118 restraints weight = 25396.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.112161 restraints weight = 16285.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.113576 restraints weight = 11751.915| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9341 Z= 0.229 Angle : 0.832 12.153 12654 Z= 0.391 Chirality : 0.045 0.335 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.983 56.135 1276 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.32 % Allowed : 5.17 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.90 (0.23), residues: 1192 helix: -0.86 (0.16), residues: 983 sheet: None (None), residues: 0 loop : -2.43 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.033 0.002 PHE X 224 TYR 0.012 0.002 TYR U 82 ARG 0.003 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 474 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 471 time to evaluate : 0.955 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: 0.8033 (mp) cc_final: 0.7554 (tp) REVERT: K 39 ARG cc_start: 0.7755 (ptm-80) cc_final: 0.7545 (ttp80) REVERT: L 39 ARG cc_start: 0.7690 (ptm-80) cc_final: 0.6689 (tmt-80) REVERT: L 47 VAL cc_start: 0.8861 (t) cc_final: 0.8537 (p) REVERT: L 66 LEU cc_start: 0.7353 (pt) cc_final: 0.6447 (mt) REVERT: M 4 VAL cc_start: 0.7257 (p) cc_final: 0.7051 (m) REVERT: M 39 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.6908 (tpm170) REVERT: M 67 MET cc_start: 0.7686 (ppp) cc_final: 0.7419 (ppp) REVERT: N 53 LEU cc_start: 0.7919 (tt) cc_final: 0.7543 (mt) REVERT: N 59 GLU cc_start: 0.8423 (tp30) cc_final: 0.8213 (tp30) REVERT: O 35 ASN cc_start: 0.8096 (t0) cc_final: 0.7796 (t0) REVERT: P 24 ILE cc_start: 0.9331 (mt) cc_final: 0.9065 (mt) REVERT: P 59 GLU cc_start: 0.8147 (tp30) cc_final: 0.7796 (tp30) REVERT: P 67 MET cc_start: 0.8322 (ppp) cc_final: 0.7854 (ppp) REVERT: Q 30 PHE cc_start: 0.8283 (m-80) cc_final: 0.7931 (m-80) REVERT: Q 64 PHE cc_start: 0.7574 (m-80) cc_final: 0.7231 (m-10) REVERT: R 43 ILE cc_start: 0.8835 (tt) cc_final: 0.8573 (tt) REVERT: R 47 VAL cc_start: 0.9212 (t) cc_final: 0.8881 (p) REVERT: S 2 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7854 (pm20) REVERT: S 39 ARG cc_start: 0.7330 (ptm160) cc_final: 0.6522 (tpt170) REVERT: T 67 MET cc_start: 0.7902 (tmm) cc_final: 0.6822 (tmm) REVERT: T 71 LEU cc_start: 0.8611 (pt) cc_final: 0.8380 (pt) REVERT: X 67 ASP cc_start: 0.8965 (m-30) cc_final: 0.8755 (m-30) REVERT: X 88 MET cc_start: 0.8131 (ttm) cc_final: 0.7812 (ttm) REVERT: X 176 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7892 (ttm110) REVERT: Z 72 TYR cc_start: 0.7203 (t80) cc_final: 0.6981 (t80) REVERT: 7 157 LYS cc_start: 0.4918 (mtpt) cc_final: 0.4695 (mtmt) REVERT: U 76 PHE cc_start: 0.6366 (t80) cc_final: 0.6139 (t80) REVERT: J 27 MET cc_start: 0.8507 (tpp) cc_final: 0.8226 (mmp) outliers start: 3 outliers final: 0 residues processed: 473 average time/residue: 0.1851 time to fit residues: 123.8440 Evaluate side-chains 395 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 0.4980 chunk 106 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.0470 chunk 105 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.130015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.110663 restraints weight = 25198.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.112632 restraints weight = 17517.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114462 restraints weight = 11776.971| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9341 Z= 0.236 Angle : 0.800 10.896 12654 Z= 0.380 Chirality : 0.045 0.357 1558 Planarity : 0.004 0.060 1537 Dihedral : 5.733 54.424 1276 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -1.41 (0.24), residues: 1192 helix: -0.50 (0.16), residues: 988 sheet: None (None), residues: 0 loop : -2.41 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 234 HIS 0.002 0.001 HIS X 114 PHE 0.026 0.002 PHE X 167 TYR 0.017 0.001 TYR U 55 ARG 0.002 0.000 ARG X 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8082 (mp) cc_final: 0.7593 (tp) REVERT: L 39 ARG cc_start: 0.7616 (ptm-80) cc_final: 0.6683 (tmt-80) REVERT: M 67 MET cc_start: 0.7694 (ppp) cc_final: 0.7246 (ppp) REVERT: N 53 LEU cc_start: 0.7964 (tt) cc_final: 0.7511 (mt) REVERT: N 59 GLU cc_start: 0.8384 (tp30) cc_final: 0.8176 (tp30) REVERT: P 24 ILE cc_start: 0.9279 (mt) cc_final: 0.9015 (mt) REVERT: P 59 GLU cc_start: 0.8179 (tp30) cc_final: 0.7884 (tp30) REVERT: P 67 MET cc_start: 0.8078 (ppp) cc_final: 0.7516 (ppp) REVERT: Q 14 ILE cc_start: 0.9267 (mt) cc_final: 0.9022 (mp) REVERT: S 2 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7623 (pm20) REVERT: S 30 PHE cc_start: 0.7273 (m-80) cc_final: 0.7048 (m-10) REVERT: S 39 ARG cc_start: 0.7345 (ptm160) cc_final: 0.6518 (tpt170) REVERT: S 57 LEU cc_start: 0.8648 (mt) cc_final: 0.8419 (mt) REVERT: S 59 GLU cc_start: 0.7790 (tp30) cc_final: 0.7560 (tp30) REVERT: S 61 THR cc_start: 0.7385 (t) cc_final: 0.7175 (t) REVERT: S 64 PHE cc_start: 0.7311 (m-10) cc_final: 0.6764 (m-10) REVERT: X 67 ASP cc_start: 0.8988 (m-30) cc_final: 0.8643 (m-30) REVERT: X 72 MET cc_start: 0.8919 (tmm) cc_final: 0.8650 (tmm) REVERT: X 88 MET cc_start: 0.8350 (ttm) cc_final: 0.8060 (ttm) REVERT: X 176 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7655 (ttm110) REVERT: X 221 MET cc_start: 0.8274 (mtt) cc_final: 0.7611 (mtt) REVERT: 7 151 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7274 (tp30) REVERT: U 76 PHE cc_start: 0.6124 (t80) cc_final: 0.5484 (m-80) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.1798 time to fit residues: 117.8445 Evaluate side-chains 390 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.108404 restraints weight = 25822.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.110426 restraints weight = 17076.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.111800 restraints weight = 12391.242| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9341 Z= 0.279 Angle : 0.841 10.452 12654 Z= 0.405 Chirality : 0.046 0.390 1558 Planarity : 0.005 0.062 1537 Dihedral : 5.730 55.453 1276 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -1.23 (0.24), residues: 1192 helix: -0.42 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.40 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.046 0.002 PHE Q 64 TYR 0.014 0.002 TYR S 9 ARG 0.007 0.001 ARG K 39 *********************** 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 441 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.993 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: 0.8162 (mp) cc_final: 0.7709 (tp) REVERT: K 67 MET cc_start: 0.7821 (tmm) cc_final: 0.7522 (tmm) REVERT: L 39 ARG cc_start: 0.7814 (ptm-80) cc_final: 0.6783 (tmt-80) REVERT: M 45 ASP cc_start: 0.7882 (m-30) cc_final: 0.7553 (p0) REVERT: M 67 MET cc_start: 0.7818 (ppp) cc_final: 0.7405 (ppp) REVERT: N 53 LEU cc_start: 0.7962 (tt) cc_final: 0.7490 (mt) REVERT: P 67 MET cc_start: 0.8054 (ppp) cc_final: 0.7575 (ppp) REVERT: Q 39 ARG cc_start: 0.7938 (ptp90) cc_final: 0.7672 (ptp90) REVERT: Q 64 PHE cc_start: 0.7847 (m-80) cc_final: 0.7562 (m-80) REVERT: R 4 VAL cc_start: 0.8606 (m) cc_final: 0.8390 (p) REVERT: R 8 LYS cc_start: 0.7874 (mmtp) cc_final: 0.7623 (tppt) REVERT: R 47 VAL cc_start: 0.9247 (t) cc_final: 0.8857 (p) REVERT: S 2 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7826 (pp30) REVERT: S 30 PHE cc_start: 0.7354 (m-80) cc_final: 0.7083 (m-10) REVERT: S 39 ARG cc_start: 0.7570 (ptm160) cc_final: 0.6514 (tpt170) REVERT: S 59 GLU cc_start: 0.7782 (tp30) cc_final: 0.7574 (tp30) REVERT: S 64 PHE cc_start: 0.7375 (m-10) cc_final: 0.6973 (m-10) REVERT: X 67 ASP cc_start: 0.8899 (m-30) cc_final: 0.8621 (m-30) REVERT: X 71 ASN cc_start: 0.8306 (m-40) cc_final: 0.7977 (m-40) REVERT: X 88 MET cc_start: 0.8364 (ttm) cc_final: 0.8151 (ttm) REVERT: X 176 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7913 (ttm110) REVERT: X 221 MET cc_start: 0.8357 (mtt) cc_final: 0.7694 (mtt) outliers start: 1 outliers final: 1 residues processed: 440 average time/residue: 0.1888 time to fit residues: 118.1718 Evaluate side-chains 383 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.130816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111062 restraints weight = 26119.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.113250 restraints weight = 17039.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.114761 restraints weight = 12276.836| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9341 Z= 0.222 Angle : 0.820 13.126 12654 Z= 0.386 Chirality : 0.045 0.318 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.566 52.484 1276 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -0.92 (0.24), residues: 1192 helix: -0.20 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.45 (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 0.035 0.002 PHE Q 64 TYR 0.014 0.001 TYR 8 15 ARG 0.006 0.001 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 450 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8093 (mp) cc_final: 0.7670 (tp) REVERT: L 39 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.6892 (tmt-80) REVERT: L 67 MET cc_start: 0.7474 (mmt) cc_final: 0.7204 (mmt) REVERT: M 45 ASP cc_start: 0.7826 (m-30) cc_final: 0.7617 (p0) REVERT: M 67 MET cc_start: 0.7838 (ppp) cc_final: 0.7465 (ppp) REVERT: N 53 LEU cc_start: 0.7789 (tt) cc_final: 0.7490 (mt) REVERT: P 67 MET cc_start: 0.8323 (ppp) cc_final: 0.7784 (ppp) REVERT: Q 30 PHE cc_start: 0.8240 (m-80) cc_final: 0.8012 (m-80) REVERT: Q 35 ASN cc_start: 0.8106 (m-40) cc_final: 0.7395 (m-40) REVERT: Q 64 PHE cc_start: 0.7718 (m-80) cc_final: 0.7513 (m-80) REVERT: R 8 LYS cc_start: 0.7867 (mmtp) cc_final: 0.7607 (tppt) REVERT: R 47 VAL cc_start: 0.9295 (t) cc_final: 0.8957 (p) REVERT: R 65 CYS cc_start: 0.7589 (t) cc_final: 0.7334 (t) REVERT: S 2 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7526 (pp30) REVERT: S 30 PHE cc_start: 0.7211 (m-80) cc_final: 0.6945 (m-10) REVERT: S 39 ARG cc_start: 0.7629 (ptm160) cc_final: 0.6506 (tpt170) REVERT: S 59 GLU cc_start: 0.7942 (tp30) cc_final: 0.7719 (tp30) REVERT: T 72 LEU cc_start: 0.8757 (tp) cc_final: 0.8531 (tp) REVERT: X 67 ASP cc_start: 0.8994 (m-30) cc_final: 0.8597 (m-30) REVERT: X 70 MET cc_start: 0.7396 (tpt) cc_final: 0.6998 (tpt) REVERT: X 176 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7841 (ttm110) REVERT: X 221 MET cc_start: 0.8326 (mtt) cc_final: 0.7675 (mtt) REVERT: X 223 GLU cc_start: 0.8641 (pp20) cc_final: 0.8367 (pp20) REVERT: 7 144 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7115 (tm-30) REVERT: 7 157 LYS cc_start: 0.5521 (mtmt) cc_final: 0.4980 (tttm) REVERT: U 76 PHE cc_start: 0.6071 (t80) cc_final: 0.5480 (m-80) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1772 time to fit residues: 115.6845 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 : 0.976 ------------------------------------------------------------------------------- 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: 0.7980 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 180 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 = 0.4104 r_free = 0.4104 target = 0.131351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111327 restraints weight = 26058.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.113478 restraints weight = 16767.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.114910 restraints weight = 12084.090| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9341 Z= 0.228 Angle : 0.834 11.977 12654 Z= 0.392 Chirality : 0.045 0.409 1558 Planarity : 0.004 0.064 1537 Dihedral : 5.460 50.417 1276 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.66 (0.24), residues: 1192 helix: -0.02 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.34 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.032 0.002 PHE Q 64 TYR 0.025 0.002 TYR M 9 ARG 0.005 0.000 ARG X 169 *********************** 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 445 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8146 (mp) cc_final: 0.7734 (tp) REVERT: L 39 ARG cc_start: 0.7537 (ptm-80) cc_final: 0.6930 (tmt-80) REVERT: L 67 MET cc_start: 0.7532 (mmt) cc_final: 0.7293 (mmt) REVERT: M 67 MET cc_start: 0.7847 (ppp) cc_final: 0.7461 (ppp) REVERT: O 5 LEU cc_start: 0.7698 (pt) cc_final: 0.7395 (mp) REVERT: O 64 PHE cc_start: 0.7369 (m-80) cc_final: 0.7127 (m-80) REVERT: P 67 MET cc_start: 0.8277 (ppp) cc_final: 0.7683 (ppp) REVERT: Q 30 PHE cc_start: 0.8222 (m-80) cc_final: 0.7962 (m-80) REVERT: Q 35 ASN cc_start: 0.8239 (m-40) cc_final: 0.7114 (m-40) REVERT: Q 64 PHE cc_start: 0.7703 (m-80) cc_final: 0.7339 (m-80) REVERT: R 8 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7639 (tppt) REVERT: R 47 VAL cc_start: 0.9313 (t) cc_final: 0.8820 (p) REVERT: S 30 PHE cc_start: 0.7189 (m-80) cc_final: 0.6894 (m-10) REVERT: S 37 VAL cc_start: 0.8875 (m) cc_final: 0.8655 (m) REVERT: S 39 ARG cc_start: 0.7502 (ptm160) cc_final: 0.6427 (tpt170) REVERT: S 59 GLU cc_start: 0.7916 (tp30) cc_final: 0.7659 (tp30) REVERT: T 72 LEU cc_start: 0.8605 (tp) cc_final: 0.8379 (tp) REVERT: 8 12 GLN cc_start: 0.8278 (tt0) cc_final: 0.7978 (tt0) REVERT: X 67 ASP cc_start: 0.8978 (m-30) cc_final: 0.8525 (m-30) REVERT: X 70 MET cc_start: 0.7399 (tpt) cc_final: 0.7065 (tpt) REVERT: X 176 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7836 (ttm110) REVERT: X 188 MET cc_start: 0.7658 (ptp) cc_final: 0.7182 (mtm) REVERT: X 221 MET cc_start: 0.8372 (mtt) cc_final: 0.7857 (mtp) REVERT: 7 157 LYS cc_start: 0.5656 (mtmt) cc_final: 0.5198 (tttm) REVERT: U 76 PHE cc_start: 0.5920 (t80) cc_final: 0.5413 (m-80) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1812 time to fit residues: 115.7367 Evaluate side-chains 379 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 4.9990 chunk 105 optimal weight: 0.0980 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.131756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111667 restraints weight = 26711.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.113775 restraints weight = 18124.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115249 restraints weight = 13209.166| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9341 Z= 0.235 Angle : 0.845 15.427 12654 Z= 0.393 Chirality : 0.044 0.237 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.371 48.744 1276 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -0.50 (0.24), residues: 1192 helix: 0.09 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.31 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 67 HIS 0.002 0.001 HIS X 137 PHE 0.027 0.002 PHE Q 64 TYR 0.012 0.001 TYR U 51 ARG 0.004 0.000 ARG X 169 *********************** 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 435 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8088 (mp) cc_final: 0.7709 (tp) REVERT: L 17 ILE cc_start: 0.8302 (pt) cc_final: 0.8055 (pt) REVERT: L 39 ARG cc_start: 0.7599 (ptm-80) cc_final: 0.6881 (tmt170) REVERT: L 67 MET cc_start: 0.7524 (mmt) cc_final: 0.7256 (mmt) REVERT: M 67 MET cc_start: 0.7869 (ppp) cc_final: 0.7443 (ppp) REVERT: O 5 LEU cc_start: 0.7564 (pt) cc_final: 0.7324 (mp) REVERT: P 67 MET cc_start: 0.8268 (ppp) cc_final: 0.7643 (ppp) REVERT: Q 35 ASN cc_start: 0.8252 (m-40) cc_final: 0.7870 (m-40) REVERT: Q 64 PHE cc_start: 0.7443 (m-80) cc_final: 0.7241 (m-80) REVERT: R 8 LYS cc_start: 0.7896 (mmtp) cc_final: 0.7676 (tppt) REVERT: R 47 VAL cc_start: 0.9248 (t) cc_final: 0.8770 (p) REVERT: S 30 PHE cc_start: 0.7124 (m-80) cc_final: 0.6823 (m-10) REVERT: S 39 ARG cc_start: 0.7557 (ptm160) cc_final: 0.6444 (tpt170) REVERT: S 59 GLU cc_start: 0.7757 (tp30) cc_final: 0.7532 (tp30) REVERT: T 72 LEU cc_start: 0.8659 (tp) cc_final: 0.8413 (tp) REVERT: X 67 ASP cc_start: 0.8956 (m-30) cc_final: 0.8577 (m-30) REVERT: X 70 MET cc_start: 0.7496 (tpt) cc_final: 0.7190 (tpt) REVERT: X 88 MET cc_start: 0.8208 (ttm) cc_final: 0.7970 (ttm) REVERT: X 176 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7723 (ttm110) REVERT: X 221 MET cc_start: 0.8413 (mtt) cc_final: 0.7901 (mtp) REVERT: Z 71 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7563 (mmtm) REVERT: 7 157 LYS cc_start: 0.5801 (mtmt) cc_final: 0.5374 (tttm) REVERT: 7 173 MET cc_start: 0.6067 (pmm) cc_final: 0.5816 (ptt) REVERT: U 50 ARG cc_start: 0.7198 (mpp-170) cc_final: 0.6982 (mpp-170) REVERT: U 76 PHE cc_start: 0.6198 (t80) cc_final: 0.5551 (m-80) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1878 time to fit residues: 117.9390 Evaluate side-chains 378 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 180 ASN U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.130772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111247 restraints weight = 25753.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.113362 restraints weight = 17045.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.114778 restraints weight = 12450.204| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9341 Z= 0.253 Angle : 0.865 15.683 12654 Z= 0.404 Chirality : 0.046 0.308 1558 Planarity : 0.004 0.065 1537 Dihedral : 5.413 47.683 1276 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.25), residues: 1192 helix: 0.18 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -2.22 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.027 0.002 PHE U 56 TYR 0.019 0.001 TYR X 232 ARG 0.003 0.000 ARG X 169 *********************** 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 432 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.990 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: 0.8097 (mp) cc_final: 0.7720 (tp) REVERT: L 5 LEU cc_start: 0.8514 (mm) cc_final: 0.8172 (mm) REVERT: L 39 ARG cc_start: 0.7622 (ptm-80) cc_final: 0.6820 (tmt170) REVERT: L 67 MET cc_start: 0.7533 (mmt) cc_final: 0.7281 (mmt) REVERT: M 67 MET cc_start: 0.7895 (ppp) cc_final: 0.7468 (ppp) REVERT: N 10 ILE cc_start: 0.8402 (tp) cc_final: 0.8090 (tp) REVERT: P 59 GLU cc_start: 0.8029 (tp30) cc_final: 0.7763 (tp30) REVERT: P 67 MET cc_start: 0.8249 (ppp) cc_final: 0.7599 (ppp) REVERT: Q 35 ASN cc_start: 0.8250 (m-40) cc_final: 0.8045 (m-40) REVERT: Q 64 PHE cc_start: 0.7542 (m-80) cc_final: 0.7313 (m-80) REVERT: R 47 VAL cc_start: 0.9172 (t) cc_final: 0.8714 (p) REVERT: S 30 PHE cc_start: 0.7190 (m-80) cc_final: 0.6862 (m-10) REVERT: S 39 ARG cc_start: 0.7569 (ptm160) cc_final: 0.6408 (tpt170) REVERT: T 72 LEU cc_start: 0.8715 (tp) cc_final: 0.8403 (tp) REVERT: X 67 ASP cc_start: 0.8932 (m-30) cc_final: 0.8578 (m-30) REVERT: X 70 MET cc_start: 0.7397 (tpt) cc_final: 0.7066 (tpt) REVERT: X 88 MET cc_start: 0.8243 (ttm) cc_final: 0.7943 (ttm) REVERT: X 221 MET cc_start: 0.8428 (mtt) cc_final: 0.7924 (mtp) REVERT: Z 71 LYS cc_start: 0.8274 (tmmt) cc_final: 0.7580 (mmtm) REVERT: 7 157 LYS cc_start: 0.6259 (mtmt) cc_final: 0.5887 (tttm) REVERT: 7 169 ASN cc_start: 0.7645 (t0) cc_final: 0.7436 (t0) REVERT: U 76 PHE cc_start: 0.6022 (t80) cc_final: 0.5464 (m-80) REVERT: J 9 ILE cc_start: 0.7914 (tp) cc_final: 0.7525 (mm) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1802 time to fit residues: 111.3833 Evaluate side-chains 374 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.132296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112825 restraints weight = 25967.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.114811 restraints weight = 17510.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.116163 restraints weight = 12883.402| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9341 Z= 0.231 Angle : 0.872 14.693 12654 Z= 0.403 Chirality : 0.045 0.247 1558 Planarity : 0.004 0.058 1537 Dihedral : 5.362 45.172 1276 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.25 (0.25), residues: 1192 helix: 0.22 (0.17), residues: 998 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.002 0.000 HIS X 137 PHE 0.026 0.002 PHE R 64 TYR 0.020 0.002 TYR U 55 ARG 0.004 0.000 ARG X 169 ********************** 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 431 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.8090 (mp) cc_final: 0.7713 (tp) REVERT: L 5 LEU cc_start: 0.8521 (mm) cc_final: 0.8255 (mm) REVERT: L 39 ARG cc_start: 0.7561 (ptm-80) cc_final: 0.6787 (tmt170) REVERT: M 67 MET cc_start: 0.8010 (ppp) cc_final: 0.7563 (ppp) REVERT: O 67 MET cc_start: 0.8044 (ppp) cc_final: 0.4926 (mtt) REVERT: O 68 VAL cc_start: 0.8551 (t) cc_final: 0.8287 (t) REVERT: P 67 MET cc_start: 0.8199 (ppp) cc_final: 0.7579 (ppp) REVERT: Q 52 ILE cc_start: 0.8662 (tt) cc_final: 0.8261 (mm) REVERT: Q 64 PHE cc_start: 0.7470 (m-80) cc_final: 0.7236 (m-80) REVERT: R 47 VAL cc_start: 0.9159 (t) cc_final: 0.8718 (p) REVERT: R 65 CYS cc_start: 0.7462 (t) cc_final: 0.7238 (t) REVERT: S 30 PHE cc_start: 0.7180 (m-80) cc_final: 0.6834 (m-10) REVERT: S 39 ARG cc_start: 0.7606 (ptm160) cc_final: 0.6408 (tpt170) REVERT: T 52 ILE cc_start: 0.6652 (mm) cc_final: 0.6312 (mm) REVERT: T 72 LEU cc_start: 0.8632 (tp) cc_final: 0.8313 (tp) REVERT: X 67 ASP cc_start: 0.8857 (m-30) cc_final: 0.8424 (m-30) REVERT: X 70 MET cc_start: 0.7463 (tpt) cc_final: 0.7142 (tpt) REVERT: X 176 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7591 (ttm-80) REVERT: X 221 MET cc_start: 0.8457 (mtt) cc_final: 0.7959 (mtp) REVERT: Z 71 LYS cc_start: 0.8433 (tmmt) cc_final: 0.7651 (mmtm) REVERT: Z 86 LYS cc_start: 0.8739 (tptp) cc_final: 0.8367 (ttmm) REVERT: 7 157 LYS cc_start: 0.6304 (mtmt) cc_final: 0.5879 (tttm) REVERT: 7 173 MET cc_start: 0.5855 (pmm) cc_final: 0.5142 (ptt) REVERT: U 50 ARG cc_start: 0.7465 (mpp-170) cc_final: 0.7063 (mpp-170) REVERT: U 76 PHE cc_start: 0.6050 (t80) cc_final: 0.5550 (m-80) REVERT: J 9 ILE cc_start: 0.7993 (tp) cc_final: 0.7720 (mm) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1759 time to fit residues: 108.8882 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 : 1.036 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** Z 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.107162 restraints weight = 26475.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108972 restraints weight = 17322.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.110116 restraints weight = 12871.144| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9341 Z= 0.327 Angle : 0.921 13.900 12654 Z= 0.439 Chirality : 0.047 0.245 1558 Planarity : 0.005 0.058 1537 Dihedral : 5.549 49.575 1276 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.25 % 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: -0.58 (0.24), residues: 1192 helix: 0.02 (0.16), residues: 1042 sheet: None (None), residues: 0 loop : -2.45 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 234 HIS 0.003 0.001 HIS X 137 PHE 0.029 0.003 PHE J 16 TYR 0.019 0.002 TYR U 55 ARG 0.003 0.001 ARG X 176 =============================================================================== Job complete usr+sys time: 3226.40 seconds wall clock time: 58 minutes 58.02 seconds (3538.02 seconds total)