Starting phenix.real_space_refine on Tue Sep 24 21:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/09_2024/6cp7_7549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/09_2024/6cp7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/09_2024/6cp7_7549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/09_2024/6cp7_7549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/09_2024/6cp7_7549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp7_7549/09_2024/6cp7_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-5461/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: 5.91, per 1000 atoms: 0.64 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 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: 0.79 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: 2.50 Time building geometry restraints manager: 2.86 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: 0.550 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.090 Process input model: 23.430 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 37 poor density : 517 time to evaluate : 0.973 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: 0.1845 time to fit residues: 139.0028 Evaluate side-chains 402 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 383 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 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 fitting. rotamer outliers: 4 poor density : 473 time to evaluate : 0.942 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: 0.7488 (mp) cc_final: 0.7244 (tp) REVERT: L 39 ARG cc_start: 0.7207 (ptm-80) cc_final: 0.6620 (tmt-80) REVERT: L 47 VAL cc_start: 0.7925 (t) cc_final: 0.7693 (p) REVERT: M 39 ARG cc_start: 0.6913 (mtt-85) cc_final: 0.6681 (tpm170) REVERT: N 53 LEU cc_start: 0.7662 (tt) cc_final: 0.7426 (mt) REVERT: O 66 LEU cc_start: 0.8159 (pt) cc_final: 0.7849 (tt) REVERT: P 24 ILE cc_start: 0.9125 (mt) cc_final: 0.8899 (mt) REVERT: P 67 MET cc_start: 0.7837 (ppp) cc_final: 0.7245 (ppp) REVERT: S 66 LEU cc_start: 0.8470 (pt) cc_final: 0.8091 (pt) REVERT: T 52 ILE cc_start: 0.6280 (mm) cc_final: 0.6036 (mm) REVERT: T 57 LEU cc_start: 0.7459 (mp) cc_final: 0.7157 (mt) REVERT: X 72 MET cc_start: 0.8396 (tmm) cc_final: 0.8051 (tmm) REVERT: X 185 HIS cc_start: 0.6739 (t70) cc_final: 0.6525 (t-90) REVERT: 7 151 GLU cc_start: 0.6921 (pp20) cc_final: 0.6534 (pp20) REVERT: J 27 MET cc_start: 0.8288 (tpp) cc_final: 0.7970 (mmp) outliers start: 4 outliers final: 1 residues processed: 475 average time/residue: 0.1833 time to fit residues: 122.7183 Evaluate side-chains 391 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN ** X 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9341 Z= 0.235 Angle : 0.833 12.409 12654 Z= 0.393 Chirality : 0.046 0.343 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.952 56.222 1276 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.43 % Allowed : 5.60 % Favored : 93.97 % 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: -1.86 (0.23), residues: 1192 helix: -0.83 (0.16), residues: 981 sheet: None (None), residues: 0 loop : -2.44 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP X 234 HIS 0.004 0.001 HIS X 185 PHE 0.031 0.002 PHE X 224 TYR 0.011 0.002 TYR 8 15 ARG 0.004 0.000 ARG S 39 *********************** 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 473 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7705 (mp) cc_final: 0.7440 (tp) REVERT: L 10 ILE cc_start: 0.8116 (mt) cc_final: 0.7894 (mt) REVERT: L 39 ARG cc_start: 0.7133 (ptm-80) cc_final: 0.6581 (tmt-80) REVERT: L 66 LEU cc_start: 0.6718 (pt) cc_final: 0.5892 (mt) REVERT: M 16 THR cc_start: 0.7883 (m) cc_final: 0.7607 (m) REVERT: P 24 ILE cc_start: 0.9093 (mt) cc_final: 0.8730 (mt) REVERT: P 67 MET cc_start: 0.7637 (ppp) cc_final: 0.7203 (ppp) REVERT: R 47 VAL cc_start: 0.8749 (t) cc_final: 0.8482 (p) REVERT: S 47 VAL cc_start: 0.8973 (t) cc_final: 0.8688 (t) REVERT: S 66 LEU cc_start: 0.8553 (pt) cc_final: 0.8343 (pt) REVERT: T 67 MET cc_start: 0.8155 (tmm) cc_final: 0.7094 (tmm) REVERT: X 88 MET cc_start: 0.7307 (ttm) cc_final: 0.6985 (ttm) REVERT: X 185 HIS cc_start: 0.6950 (t70) cc_final: 0.6744 (t-90) REVERT: U 76 PHE cc_start: 0.6161 (t80) cc_final: 0.5960 (t80) REVERT: U 80 MET cc_start: 0.5599 (tpp) cc_final: 0.5057 (mtp) REVERT: J 27 MET cc_start: 0.8431 (tpp) cc_final: 0.8056 (mmp) outliers start: 4 outliers final: 0 residues processed: 471 average time/residue: 0.1700 time to fit residues: 114.0727 Evaluate side-chains 393 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5064 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= 0.256 Angle : 0.815 12.635 12654 Z= 0.391 Chirality : 0.045 0.355 1558 Planarity : 0.005 0.063 1537 Dihedral : 5.775 55.972 1276 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.11 % Allowed : 5.38 % 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: -1.49 (0.23), residues: 1192 helix: -0.57 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.71 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.003 0.001 HIS X 185 PHE 0.028 0.002 PHE P 64 TYR 0.017 0.001 TYR U 55 ARG 0.008 0.001 ARG K 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 LEU cc_start: 0.7784 (mp) cc_final: 0.7469 (tp) REVERT: L 39 ARG cc_start: 0.7164 (ptm-80) cc_final: 0.6867 (tmt-80) REVERT: P 24 ILE cc_start: 0.9045 (mt) cc_final: 0.8725 (mt) REVERT: P 67 MET cc_start: 0.7437 (ppp) cc_final: 0.7000 (ppp) REVERT: S 30 PHE cc_start: 0.6512 (m-80) cc_final: 0.6268 (m-10) REVERT: S 57 LEU cc_start: 0.8464 (mt) cc_final: 0.8239 (mt) REVERT: S 66 LEU cc_start: 0.8508 (pt) cc_final: 0.8269 (pt) REVERT: X 176 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7424 (ttm110) REVERT: X 221 MET cc_start: 0.8563 (mtt) cc_final: 0.8188 (mtp) REVERT: U 76 PHE cc_start: 0.6022 (t80) cc_final: 0.5542 (m-80) REVERT: U 80 MET cc_start: 0.5432 (tpp) cc_final: 0.4978 (mtp) REVERT: J 27 MET cc_start: 0.8499 (tpp) cc_final: 0.8262 (mmp) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.1710 time to fit residues: 109.9107 Evaluate side-chains 377 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9341 Z= 0.249 Angle : 0.831 14.025 12654 Z= 0.394 Chirality : 0.046 0.391 1558 Planarity : 0.004 0.062 1537 Dihedral : 5.681 55.013 1276 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % 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: -1.13 (0.24), residues: 1192 helix: -0.35 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.39 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.033 0.002 PHE X 224 TYR 0.011 0.001 TYR 8 15 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 443 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 441 time to evaluate : 1.036 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: 0.7776 (mp) cc_final: 0.7550 (tp) REVERT: L 39 ARG cc_start: 0.7385 (ptm-80) cc_final: 0.6777 (tmt-80) REVERT: P 67 MET cc_start: 0.7300 (ppp) cc_final: 0.7008 (ppp) REVERT: Q 14 ILE cc_start: 0.9197 (mp) cc_final: 0.8997 (mp) REVERT: R 8 LYS cc_start: 0.7555 (mmtp) cc_final: 0.7216 (tppt) REVERT: R 47 VAL cc_start: 0.8583 (t) cc_final: 0.8305 (p) REVERT: S 30 PHE cc_start: 0.6496 (m-80) cc_final: 0.6224 (m-10) REVERT: S 66 LEU cc_start: 0.8481 (pt) cc_final: 0.8243 (pt) REVERT: T 10 ILE cc_start: 0.8446 (tp) cc_final: 0.7943 (tt) REVERT: X 71 ASN cc_start: 0.7559 (m-40) cc_final: 0.7339 (m-40) REVERT: X 88 MET cc_start: 0.7730 (ttm) cc_final: 0.7512 (ttm) REVERT: X 221 MET cc_start: 0.8642 (mtt) cc_final: 0.8227 (mtp) REVERT: 7 157 LYS cc_start: 0.5524 (mtmt) cc_final: 0.4901 (tttm) REVERT: U 76 PHE cc_start: 0.5913 (t80) cc_final: 0.5434 (m-80) REVERT: U 80 MET cc_start: 0.5491 (tpp) cc_final: 0.5115 (mtp) REVERT: J 27 MET cc_start: 0.8309 (tpp) cc_final: 0.7982 (tpt) outliers start: 2 outliers final: 0 residues processed: 442 average time/residue: 0.1816 time to fit residues: 114.8494 Evaluate side-chains 369 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 185 HIS U 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9341 Z= 0.227 Angle : 0.836 14.505 12654 Z= 0.393 Chirality : 0.045 0.296 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.538 52.872 1276 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: -0.88 (0.24), residues: 1192 helix: -0.18 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -2.28 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.045 0.002 PHE Q 64 TYR 0.025 0.002 TYR L 9 ARG 0.003 0.000 ARG K 39 *********************** 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 441 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.6998 (tmt-80) REVERT: L 67 MET cc_start: 0.6479 (mmt) cc_final: 0.6222 (mmt) REVERT: P 67 MET cc_start: 0.7826 (ppp) cc_final: 0.7233 (ppp) REVERT: R 8 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7255 (tppt) REVERT: R 47 VAL cc_start: 0.8664 (t) cc_final: 0.8429 (p) REVERT: S 30 PHE cc_start: 0.6386 (m-80) cc_final: 0.6076 (m-10) REVERT: X 71 ASN cc_start: 0.7588 (m-40) cc_final: 0.7286 (m-40) REVERT: X 88 MET cc_start: 0.7711 (ttm) cc_final: 0.7483 (ttm) REVERT: 7 144 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6696 (tm-30) REVERT: 7 157 LYS cc_start: 0.5752 (mtmt) cc_final: 0.5365 (tttm) REVERT: U 76 PHE cc_start: 0.5949 (t80) cc_final: 0.5459 (m-80) REVERT: U 80 MET cc_start: 0.5541 (tpp) cc_final: 0.5212 (mtp) REVERT: J 27 MET cc_start: 0.8229 (tpp) cc_final: 0.7969 (tpt) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.1702 time to fit residues: 108.3954 Evaluate side-chains 379 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 185 HIS Z 93 ASN U 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6007 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= 0.242 Angle : 0.846 12.720 12654 Z= 0.394 Chirality : 0.047 0.432 1558 Planarity : 0.004 0.063 1537 Dihedral : 5.496 50.999 1276 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1192 helix: -0.09 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -2.38 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 234 HIS 0.002 0.000 HIS X 137 PHE 0.028 0.002 PHE U 56 TYR 0.026 0.002 TYR M 9 ARG 0.003 0.000 ARG Q 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 1.003 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: L 67 MET cc_start: 0.6566 (mmt) cc_final: 0.6198 (mmt) REVERT: M 67 MET cc_start: 0.6968 (ppp) cc_final: 0.6485 (ppp) REVERT: P 67 MET cc_start: 0.7684 (ppp) cc_final: 0.7121 (ppp) REVERT: R 47 VAL cc_start: 0.8624 (t) cc_final: 0.8225 (p) REVERT: S 30 PHE cc_start: 0.6336 (m-80) cc_final: 0.6125 (m-10) REVERT: S 47 VAL cc_start: 0.8867 (t) cc_final: 0.8547 (t) REVERT: 8 12 GLN cc_start: 0.7070 (tt0) cc_final: 0.6547 (tt0) REVERT: 7 151 GLU cc_start: 0.7378 (pt0) cc_final: 0.7079 (tp30) REVERT: 7 157 LYS cc_start: 0.5715 (mtmt) cc_final: 0.5399 (tttm) REVERT: U 76 PHE cc_start: 0.5886 (t80) cc_final: 0.5438 (m-80) REVERT: J 27 MET cc_start: 0.8269 (tpp) cc_final: 0.7992 (tpt) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.1731 time to fit residues: 109.2880 Evaluate side-chains 375 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN Q 35 ASN 8 12 GLN X 185 HIS ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9341 Z= 0.239 Angle : 0.856 15.352 12654 Z= 0.399 Chirality : 0.045 0.189 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.437 49.639 1276 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -0.55 (0.24), residues: 1192 helix: 0.05 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.27 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 234 HIS 0.002 0.000 HIS X 137 PHE 0.026 0.002 PHE X 167 TYR 0.013 0.001 TYR S 9 ARG 0.003 0.000 ARG X 176 *********************** 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 438 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 1.168 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: L 67 MET cc_start: 0.6611 (mmt) cc_final: 0.6306 (mmt) REVERT: M 67 MET cc_start: 0.7011 (ppp) cc_final: 0.6720 (ppp) REVERT: P 67 MET cc_start: 0.7663 (ppp) cc_final: 0.7094 (ppp) REVERT: R 47 VAL cc_start: 0.8654 (t) cc_final: 0.8246 (p) REVERT: S 37 VAL cc_start: 0.8347 (m) cc_final: 0.8121 (m) REVERT: 8 12 GLN cc_start: 0.6955 (tt0) cc_final: 0.6462 (tt0) REVERT: 8 25 ILE cc_start: 0.8803 (mt) cc_final: 0.8572 (mt) REVERT: X 88 MET cc_start: 0.7363 (ttm) cc_final: 0.7071 (ttm) REVERT: X 188 MET cc_start: 0.7078 (ptp) cc_final: 0.6167 (mtm) REVERT: X 221 MET cc_start: 0.8660 (mtt) cc_final: 0.8290 (mtp) REVERT: 7 151 GLU cc_start: 0.7235 (pt0) cc_final: 0.6990 (tp30) REVERT: 7 157 LYS cc_start: 0.6041 (mtmt) cc_final: 0.5742 (tttm) REVERT: U 76 PHE cc_start: 0.5717 (t80) cc_final: 0.5468 (m-80) REVERT: J 27 MET cc_start: 0.8262 (tpp) cc_final: 0.7990 (tpt) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1736 time to fit residues: 109.5859 Evaluate side-chains 373 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9341 Z= 0.239 Angle : 0.892 15.283 12654 Z= 0.415 Chirality : 0.046 0.237 1558 Planarity : 0.004 0.061 1537 Dihedral : 5.449 47.765 1276 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -0.49 (0.24), residues: 1192 helix: 0.07 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -1.83 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.029 0.002 PHE U 56 TYR 0.018 0.002 TYR X 66 ARG 0.009 0.001 ARG X 176 *********************** 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 439 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 MET cc_start: 0.6628 (mmt) cc_final: 0.6337 (mmt) REVERT: M 14 ILE cc_start: 0.8331 (mm) cc_final: 0.8122 (mm) REVERT: M 67 MET cc_start: 0.7137 (ppp) cc_final: 0.6765 (ppp) REVERT: N 4 VAL cc_start: 0.7270 (p) cc_final: 0.7048 (p) REVERT: P 67 MET cc_start: 0.7690 (ppp) cc_final: 0.7116 (ppp) REVERT: R 47 VAL cc_start: 0.8538 (t) cc_final: 0.8166 (p) REVERT: X 67 ASP cc_start: 0.8319 (m-30) cc_final: 0.7943 (m-30) REVERT: Z 71 LYS cc_start: 0.8238 (tmmt) cc_final: 0.7504 (mmtm) REVERT: U 50 ARG cc_start: 0.7059 (mpp-170) cc_final: 0.6809 (mpp-170) REVERT: J 27 MET cc_start: 0.8250 (tpp) cc_final: 0.7943 (tpt) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1756 time to fit residues: 111.2312 Evaluate side-chains 368 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 12 GLN ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 HIS U 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.6643 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= 0.240 Angle : 0.891 14.621 12654 Z= 0.415 Chirality : 0.047 0.373 1558 Planarity : 0.004 0.058 1537 Dihedral : 5.426 44.643 1276 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % 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: -0.39 (0.25), residues: 1192 helix: 0.15 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -2.16 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.026 0.002 PHE R 64 TYR 0.029 0.002 TYR K 9 ARG 0.002 0.000 ARG Q 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 1.380 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: L 67 MET cc_start: 0.6642 (mmt) cc_final: 0.6442 (mmt) REVERT: M 67 MET cc_start: 0.7334 (ppp) cc_final: 0.6913 (ppp) REVERT: N 10 ILE cc_start: 0.7996 (tp) cc_final: 0.7737 (tp) REVERT: O 67 MET cc_start: 0.7448 (ppp) cc_final: 0.4174 (mtt) REVERT: O 68 VAL cc_start: 0.8221 (t) cc_final: 0.7974 (t) REVERT: P 67 MET cc_start: 0.7598 (ppp) cc_final: 0.7022 (ppp) REVERT: R 47 VAL cc_start: 0.8516 (t) cc_final: 0.8165 (p) REVERT: R 65 CYS cc_start: 0.6978 (t) cc_final: 0.6756 (t) REVERT: S 30 PHE cc_start: 0.6372 (m-80) cc_final: 0.6115 (m-80) REVERT: S 64 PHE cc_start: 0.7204 (m-10) cc_final: 0.6961 (m-10) REVERT: X 67 ASP cc_start: 0.8357 (m-30) cc_final: 0.7934 (m-30) REVERT: X 92 LEU cc_start: 0.7976 (mt) cc_final: 0.7161 (mt) REVERT: Z 71 LYS cc_start: 0.8361 (tmmt) cc_final: 0.7611 (mmtm) REVERT: Z 86 LYS cc_start: 0.8311 (tptp) cc_final: 0.8011 (ttmm) REVERT: J 27 MET cc_start: 0.8204 (tpp) cc_final: 0.7947 (tmm) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.1839 time to fit residues: 115.2453 Evaluate side-chains 365 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.113008 restraints weight = 25857.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.115159 restraints weight = 17180.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.116594 restraints weight = 12610.593| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9341 Z= 0.240 Angle : 0.895 14.478 12654 Z= 0.415 Chirality : 0.046 0.272 1558 Planarity : 0.004 0.058 1537 Dihedral : 5.348 42.280 1276 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -0.32 (0.25), residues: 1192 helix: 0.20 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -2.34 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 234 HIS 0.002 0.001 HIS X 137 PHE 0.026 0.002 PHE R 64 TYR 0.017 0.002 TYR X 66 ARG 0.002 0.000 ARG Q 39 =============================================================================== Job complete usr+sys time: 2526.25 seconds wall clock time: 46 minutes 1.53 seconds (2761.53 seconds total)